INSTRUCTION stringlengths 48 14.1k | RESPONSE stringlengths 14 8.79k | SOURCE stringclasses 1
value | METADATA stringlengths 48 55 |
|---|---|---|---|
I simulated reads for a list of variant sites using GATK SimulateReadsForVariants tool. From that, I get a bam file output. Next I create a pileup using samtools mpileup.
samtools mpileup -t DP,DPR,DV,INFO/DPR -vuf GRCh37.fa -l snp.file.vcf simreads.bam > simreads.raw.vcf
The problem is that the output is not giv... | I figured out the solution myself. I had simulated more error in my reads than I initially thought. For anyone else experiencing a similar issue, check the `-Q`, `--min-BQ` mpileup flag. Samtools automatically does not count reads in the other tags unless they are "high quality" (i.e. have a minimum base quality of 13)... | biostars | {"uid": 153026, "view_count": 3328, "vote_count": 1} |
Hi,
I have some RNA-seq samples that I want to normalize and then output RPKM expression, but I am unsure how to do this.
This is my pipeline so far:
Normalise raw read counts with TMM in edgeR
expr <- DGEList(counts=data, group=conditions)
expr <- calcNormFactors(expr)
output:
$samples
... | The library size normalized counts are made by dividing the counts by the normalization factor (you'll note that the larger libraries have larger normalization factors, so if you multiplied things you'd just inflate the difference in sequencing depth).
For the rpkms, just do `rpkm(expr, gene.length=vector)`, since i... | biostars | {"uid": 99310, "view_count": 25909, "vote_count": 8} |
Hi,
My question may seem so simple. Could you tell me what is the difference between aligning and mapping the short reads to the reference genome?
And also what is the difference between Pairwise alignment, Multiple sequence alignment and Short-Read Sequence Alignment?
Thanks | For your second question, pairwise alignment (e.g., Smith and Waterman) is between two sequences and multiple sequence alignment between more than 2 sequences (e.g., clustalW). Short read aligners are usually pairwise! | biostars | {"uid": 180986, "view_count": 19615, "vote_count": 30} |
This seems simple maths behind, But I always get confused with the terminology of **"Fold change", "Log Fold Change" *(LFC)*, and "Percentage of Change"**., When I see some of the figure descriptions given in **volcano plots**, specially X axis, I get confused.
i.e. [Page 64][1]
<a href="https://ibb.co/LtmQF2Q... | All the figures you posted above shows same thing which is Log2(FoldChange). Although 1st figure x axis labeled "Fold Change" it is Log2(FoldChange). Without log you cannot have negative values (It means down regulated genes).
One of the reasons to use log2(FoldChange) and not FoldChange only is to use same magnitu... | biostars | {"uid": 405277, "view_count": 11194, "vote_count": 3} |
Dear Biostars,
Could I please know, If there is some way to view the reads in BAM file according to user defined Insert Size range. I would like to visualize all the reads falling between certain Insert Size ranges, not all the reads.
Your ideas and resources would help me a lot. Thanks in advance.
~Prakki Rama. | <p>This is a hack but it might be good enough? Parse the input bam to extract alignments within a given *template* size range, here between 0 and 200:</p>
<pre>
<code>samtools view -h read.pe.bam \
| awk '{if (($0 ~ /^@/) || (sqrt($9^2) > 0 && sqrt($9^2) < 200)) {print $0}}' \
| samtools vie... | biostars | {"uid": 104919, "view_count": 3111, "vote_count": 1} |
Really simple question but for some reason I cannot find a simple answer to this.
We are moving from SGE to SLURM on our HPC. On SGE, we often submit a job with a range of threads, then inside the job, read the number of threads we got and use that to configure multithreaded programs. Example:
$ cat test.sh
... | You can't use a range of threads, you must state how many you need. The program you run in the script only knows how many threads you've allocated if you tell it. It is completely possible to lie to slurm and say:
#SBATCH -c 1
bowtie2 -p 20 ...
Jobs won't be killed for using too much CPU (it's often impo... | biostars | {"uid": 337120, "view_count": 8771, "vote_count": 2} |
I'm having problems with **quality score recalibration** using **GATK** as most tutorials/examples use an old version of GATK which has different syntax and arguments to the current version.
I have run this to get a recalibration table, which I think I need to get the recalibrated BAM files:
gatk-4.1.2.0/gatk... | you should use ApplyBQSR :
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_bqsr_ApplyBQSR.php
gatk BaseRecalibrator \
-I input.bam \
-R reference.fasta \
--known-sites sites_of_variation.vcf \
--known-sit... | biostars | {"uid": 383555, "view_count": 4659, "vote_count": 1} |
<p>DESeq2 gives logFC values based on fitted model. We can also get the normalized counts for each sample based on the raw counts and normalization factors, thus we can calculate the logFC ourselves using normalized counts. The question is how to report the final result. I prefer the logFC+pval/FDR from the fitted mode... | Please ignore your colleagues, they're doing it wrong.
One of the benefits of DESeq2 is that it shrinks fold-changes (toward a Gaussian prior if I remember correctly), which should increase their reliability. This is discussed and tested in [the preprint][1], which I advise everyone that uses DESeq2 to read (for a pap... | biostars | {"uid": 110060, "view_count": 5906, "vote_count": 4} |
<p>I always assumed the designations of "forward" and "reverse" strand on DNA were chosen arbitrarily (i.e. the strands could just as easily have been named the other way around).</p>
<p>However, a quick browse of the chromosome maps for Human on the NCBI map viewer seems to imply that in all cases, base numbering sta... | > ...does this mean that, for humans at least, there is a policy whereby the forward strand is always the one which contains the centromere at the lowest numerical index?
Yes, in humans the centromere is always closest to the start coordinate of each chromosome, since human chromosomes are oriented based on their p ... | biostars | {"uid": 3908, "view_count": 12710, "vote_count": 18} |
**Background**
I have paired-end RNA-seq reads from a drug-treatment experiment, with < 15 million mapped reads in many samples (too few reads) and large variability in mapped reads across biological replicates. Differential expression and splicing analysis on these samples indicate that statistical power in my test... | As you suggested (and confirmed by genomax2) it's probably the best to check using PCA if your two runs result in approximately the same result.
But as soon as you have determined it's okay I would suggest to merge your bam files, and repeat the counting before you do your final analysis. That would minimize your ch... | biostars | {"uid": 252552, "view_count": 6911, "vote_count": 1} |
I don't know how stupid of a question this is so please bear with me. I have a certain number of EST cDNA sequences that I used for miRNA prediction. The results are cDNA sequences so for the secondary structure prediction of precursor miRNA, should I use the RNA folding form or the DNA folding form on Mfold because it... | I think you should use RNA parameters because miRNAs are indeed RNA, that doesn't depend on how the sequence was acquired. | biostars | {"uid": 144783, "view_count": 3424, "vote_count": 2} |
Hi all.
I think that p-value is one of the most greatest way of measuring degree of observed data.
However, BLAST doesn't use p-value but E-value.
Why the BLAST use e-value for interpreting sequence data instead of p-value?
Is there any logical reason to use E-value for BLAST? If so, could you tell me the detail re... | <p>Quote from the BLAST help (http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html#head4 ):</p>
<p><em>"The BLAST programs report E-value rather than P-values because it is easier to understand the difference between, for example, E-value of 5 and 10 than P-values of 0.993 and 0.99995. However, when E <... | biostars | {"uid": 138612, "view_count": 13389, "vote_count": 1} |
Hi,
I was wondering if there is a way I can generate junctions.bed file from hisat2 just like the one in tophat.
Hisat2 documentation says use extract_splice_site.py python script but that gets splice site from gtf file, is there a way to know splice sites and no of reads associated with those sites using ... | Easiest solution will be to use [featureCounts][1] and counts reads from exon-exon junctions by providing your aligned BAM files. Check manual [page 35][2] for detailed information.
**-J (juncCounts)** Count the number of reads supporting each exon-exon junction.
Junctions are identified from those exon-... | biostars | {"uid": 240537, "view_count": 4318, "vote_count": 1} |
Hello everyone,
I have a bunch of TARGET samples but the associated annotation lacks the tissue information i.e. whether it is a Primary tumor or Recurrent etc. I know the value for a couple codes like `01` stands for Primary solid tumors, but I want to define the tissue type for every code for future references. Do... | Hey Komal, how are you? Say hi to Pichai!
The TCGA one was gone, but this should help.
https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes | biostars | {"uid": 220573, "view_count": 1784, "vote_count": 1} |
In Jellyfish's original paper(Marcais et al, Bioinformatics 2011), it says that "counting kmers up to 31 bases in length".
But on the other hand, in other papers such as KMC2 (Deorowicz et al, Bioinformatics 2015), Jellyfish2 is used to count kmer size = 55.
So does Jellyfish support k > 31 now? and How it is su... | Probably because they originally used 64bits per kmer, which can store up to 32 bases in 2bit (less one for whatever reason, probably to signal reverse complementation or variable-lengths).
With an update, this man-made constraint was removed. | biostars | {"uid": 243272, "view_count": 2049, "vote_count": 2} |
hello
I have a question while i am reading a paper that is related to a gene fusion discovery.
below is some of the paper's content.
> A paired end read will be a member of multiple valid clusters as a result of homology between genes, exon redundancy between transcripts, and the multiplicity of valid clusterings. F... | The problem that the authors are trying to address is the problem of false positive results in the setting of reads that can map to multiple locations. They are suggesting to use a heuristic that takes all the data available and seeks a minimal set of fusions from the set of all potential fusions. So, I believe "minimi... | biostars | {"uid": 107854, "view_count": 1997, "vote_count": 1} |
Hello. I have various .bed and .tped files (+ corresponding .fam/.tfam files) that I am exporting in vcf format from plink as follows:
./plink --tfile examplesnps --chr-set 39 --out exported_vcf --recode vcf
However, I don't know how to get an output that has the sample IDs attached to the genotype data. Doe... | Have you tried `--recode vcf-iid`? | biostars | {"uid": 446467, "view_count": 1221, "vote_count": 1} |
I am a completely rookie on Bioinformatics, so please bear with me and use simple language (I am a computer scientist) :-)
How can we use k-mers to find out if a gene is similar to our query string?
For example: We have a reference gene r = `ACAAGTC`, and a query string q = `CATGT`. For sequence alignment we could ge... | You wouldn't generally use kmers this short as the odds of finding spurious matches becomes massive, but I accept that this is a toy example.
To my knowledge, we don't really approach a sequence alignment with kmers, though you might use them to seed the alignment (in a **local** alignment, small subregions of alignme... | biostars | {"uid": 485136, "view_count": 2513, "vote_count": 1} |
Dear all,
I have FASTQ files and on start of my read I have 7 nucleotides tag - I would like to extract reads with this specific tag.
I would like to search in first 15 nucleotides of my reads, if match - extract this read to new fastq files.
Thank you for any ideas or help. | You can use Heng Li's <a href="https://github.com/lh3/bioawk">bioawk</a>:
To check if the tag is part of the first 15 bases
bioawk -c fastx 'substr($seq,0,15) ~ /$TAG/ { print }' reads.fq.gz
To match the first 7 bases to your tag,
bioawk -c fastx 'substr($seq,0,7) == $TAG { print }' reads.fq.gz | biostars | {"uid": 141203, "view_count": 10662, "vote_count": 2} |
Hi everyone,
I am trying to found out what residues are in contact with a ligand (the binding site) in a PDB file. To give you an example, I need to find the residues in contact with FMN ligand in the PDB entry 1AL7.
First of all, can we find this type of information in a PDB file? Or do we need a software to cal... | Yes, you can use the information in STRUCT_SITE_GEN listed under AC1 to get the binding residues: TYR24, TYR25, ALA76 etc.
If you did want to do this from the coordinate data, one way would be to use [BioStructures.jl][1] in Julia:
using BioStructures
struc = read("1AL7.cif", MMCIF)
res = collectres... | biostars | {"uid": 425276, "view_count": 1418, "vote_count": 1} |
Hi I have a question regarding when steps are able to run in parallel. We noticed that sometimes all of the jobs from a scatter must complete before moving to the next
I was wondering whether a scattered subworkflow can start before all the inputs to that step are available, or does a subworkflow have to wait for a... | All inputs for the step have to be available. See [this][1], look for bullet point "Instead of scattering separate steps, prefer to scatter over a subworkflow."
[1]: https://doc.arvados.org/user/cwl/cwl-style.html | biostars | {"uid": 339055, "view_count": 1007, "vote_count": 1} |
Any tool that can do median per base coverage over pre-defined windows from a BAM file?
I could make the actual per base coverage using `samtools depth` or `genomeCoverageBed`.
chr pos read_depth
1 1 6
1 2 8
...
I already have the windows prepared using
bedtools makewindows \
... | I 've written : http://lindenb.github.io/jvarkit/BamStats04.html
$ java -jar dist/bamstats04.jar -B src/test/resources/toy.bed.gz src/test/resources/toy.bam 2> /dev/null | column -t
#chrom start end length sample mincov maxcov meancov mediancov nocoveragebp percentcovered
ref 10 ... | biostars | {"uid": 293520, "view_count": 3605, "vote_count": 1} |
Is there an option in Hisat that is similar to `-g`/`--max-multihits` in Tophat? I can not find it in the parameter list on https://ccb.jhu.edu/software/hisat/manual.shtml#options. There is a Uniqueness class in here: https://github.com/infphilo/hisat/blob/master/unique.h, but when I grep for that class or the `bestIsU... | <p>The most recent release of hisat (v0.1.6) uses NH tags in the BAM to specify the number of alignments for the read/pair (see release notes: <a href="https://ccb.jhu.edu/software/hisat/index.shtml">https://ccb.jhu.edu/software/hisat/index.shtml</a>). As far as I understand it, reads/pairs with NH:i:1 have a single be... | biostars | {"uid": 148289, "view_count": 7316, "vote_count": 1} |
I'm using ete toolkit to get a phylogenetic tree for a list of ncbi taxids:
```py
from ete2 import NCBITaxa
ncbi = NCBITaxa()
tree = ncbi.get_topology([9606, 9598, 10090, 7707, 8782])
print tree.get_ascii(attributes=["sci_name", "rank"])
```
Printing it with ascii chars works, but how to render this tree *including* ... | `tree.render()` is a general purpose method. As node attributes are completely arbitrary, you need to specify what should be drawn and where... Check the docs regarding the drawing system: https://pythonhosted.org/ete2/tutorial/tutorial_drawing.html
For your example, something like this should work:
```py
from ete2 i... | biostars | {"uid": 153788, "view_count": 4108, "vote_count": 1} |
I have an amalgamated BCF file, containing the variant calls from the FULL GENOME of 70 individuals.
I've run the command ...
bcftools view -i 'TYPE="snp" && AC=140 && GT="hom" && QUAL>20' ./<filename>.bcf | wc -l
This should (and based on the output lines I've looked at - does) respond with any variant... | The ALT and REF SNPs do not always correspond to the Major/Minor allele at a SNP position. Thus, in some cases the major allele = ALT allele. This could be driving the numbers you are seeing. The other thing that could be driving these numbers is if al 70 patients are of similar ethnicity. I would recommend lookin... | biostars | {"uid": 281202, "view_count": 1371, "vote_count": 1} |
Hi folks!
I have two GFF3 files, one with annotated genes. Another with predicted transposons.
I want to find the numerical distribution of the distances between transposons and genes.
I already found the distance amongst just transposons, and amongst just genes - using the 'spacing' sub-command of bedtools 2.2.4.0,... | Maybe `closestBed` with `-d` option is what you want?
```
Tool: bedtools closest (aka closestBed)
Version: v2.23.0
Summary: For each feature in A, finds the closest
feature (upstream or downstream) in B.
...
-d In addition to the closest feature in B,
report its distance to A as an extra ... | biostars | {"uid": 147099, "view_count": 1594, "vote_count": 1} |
What happened with miRecords mirna database website? The webpage is not available and I used it's data as part of an analysis in my paper. Now the reviewer can't see the page and asks for an explanation.
Edit:
Sorry, I forgot to post the link. The miRecords was suppose to be available at http://miRecords.umn.edu/miRe... | <p>http://mirecords.umn.edu/miRecords/ works fine for me at this moment. It may just have been a hiccup.</p>
| biostars | {"uid": 110420, "view_count": 5805, "vote_count": 3} |
<p>Hi all,</p>
<p>I'm dealing with a fasta file with spaces at the end of line, which caused the problem. I didn't find a suitable way to remove them. Please kindly tell me the appropriate command for removing them?</p>
| Oh my gawk!
All previous solutions would risk modifying your fasta header as well. This one will not.
gawk 'BEGIN{line=0}{ if ($0 !~/^>/ && $0 ~/ +/ ) {gsub(/ +/, //); line++} print}END{print line" lines with white spaces treated" > "/dev/stderr"}' myfasta.fa >output.fa
If you only want to remove the space... | biostars | {"uid": 170941, "view_count": 14145, "vote_count": 1} |
I am trying to run MutSIgCV and got stuck with this error:
```
MutSigCV allsamples.md.tc.ir.br.pr.ug.dbsnp.vep.maf \
"$anno"exome_full192.coverage.txt \
"$anno"gene.covariates.txt \
my_results \
"$anno"mutation_type_dictionary_file.txt \
"$anno"chr_files_hg19
======================================
MutSigCV
v1.4
(c) ... | <a href="https://github.com/mskcc/vcf2maf">vcf2maf</a> doesn't support multi-sample VCFs, like the sample you've shown. When `--tumor-id` is not specified, the resulting MAF will name all the samples as `TUMOR`... which is why MutSig thinks you have a single patient. Even though you're not working with cancer, it is pe... | biostars | {"uid": 108112, "view_count": 9400, "vote_count": 1} |
Hello everyone (first post ever for me)
I am using Biomart in R and I am trying to obtain the maize homologs of a set of barley genes (I am only displaying one here for example's sake). Everything works fine when I use the getBM function for getLDS does not seem to work.
```r
host="plants.ensembl.org"
mysets<-listDat... | Great spot that this was related to the `virtualSchemaName`. That was hardcoded to be `"default"` in **biomaRt** and no one has ever reported a problem before. I assumed there were no Mart instances that ever used anything different!
Anyway, it's been patched in **biomaRt** version 2.50.3, which should be availabl... | biostars | {"uid": 9507620, "view_count": 1178, "vote_count": 1} |
I am using BWA to align files. I have four directories: seqtk_1, seqtk_2, seqtk_3, seqtk_4. Within each of those directories I have 10 subdirectories: subsample_1, subsample_2, subsample_3, etc. Within each of those subdirectories I have 20 paired-end reads (so from 10 genomes).
I want to put all the files from the... | You should parse the seqtk folder and subsample folder directly from `$filename` - see bellow for a suggestion. Your second and third for loops are already contained in the first:
First loop:
for filename in ./Mock_Run/seqtk_*/subsample_*/*_1.fq.gz;
Second loop:
for i in $(seq 10 $END);
do ech... | biostars | {"uid": 269775, "view_count": 2738, "vote_count": 2} |
Hi guys,
The genotype imputation need human genetic map file, whose format is like(in chr1):
position COMBINED_rate(cM/Mb) Genetic_Map(cM)
55550 0 0
568322 0 0
568527 0 0
721290 2.685807669 0.410292036939447
723819 2.8222713027 0.417429561063975
723891 2.9813105581 0.417644215424... | Hi, Tao.
Let's take the 4th row as an example.
1. 721290 means the 721290th position on chr1 and also means 0.721290 Mb.
2. To find 2nd column you need not numbers from 1st and 3d columns, but results of the subtractions: in the 4th row, it will be (0.41...-0)/(0.721290-0.568527) which gives us 2.685807669. So,... | biostars | {"uid": 222697, "view_count": 6942, "vote_count": 5} |
If I made a fake fasta with 10x the material of a book, randomly cut and spliced, and use this to align a Book, could tophat2 reconstruct the book? Or it only work with with ATCG letters?
Just a question that came out in my mind today. | You would need to re-encode the book as ACGT. For example, 1 ASCII character is 8 bits, corresponding to 4 nucleotides if you use the simplest possible encoding (rather than trying to pack into 7 or 6.5 bits, or whatever). Thus for an ASCII-formatted text file of the book, the encoded book would be 4x as long, but the ... | biostars | {"uid": 146643, "view_count": 1899, "vote_count": 5} |
Hello clever community!
I need your advice.
I am working on a *de novo* plant genome assembly of ~400 Mb.
I have Chromium 10x data, which was assembled with supernova. I also have Illumina paired end reads. Now I have additional data of PacBio reads, 120x roughly. The genome is diploid and I am thinking about usi... | Falcon is not a bad choice, an alternative might be Canu (if you have the computational resources for it)
1) MEDUSA (as well as QuickMerge) is one of those integrating assembly/scaffolding tools
3) Pilon, Arrow, and there will be others I guess
4) Canu, but with the same remark as https://www.biostars.org/u/2... | biostars | {"uid": 324156, "view_count": 3032, "vote_count": 2} |
I am working on a project comparing RNAseq quantification results between Illumina short-reads and Nanopore long-reads and I have a couple questions about comparing the quantification results from these two technologies. More specifically I need some help with figuring out how to normalize the data for the comparisons ... | I did some work on this area before, it definitely has a lot of challenges.
The biggest difference, is short reads RNAseq measurement are calculated considering the transcript length (normalized against it).
The long reads tools does not normalized to transcript length. The reads are the actual transcripts, if you ar... | biostars | {"uid": 9552419, "view_count": 268, "vote_count": 2} |
Since phylogenetic analysis largely depends on a quality of primary sequence data I usually curate alignments manually and exclude phylogenetically uninformative or misleading sites.
But do you know any tool that could tell me how good my alignment is before sending it to phylogenetic program? Are there any programs o... | The 'quality' of an alignment is somewhat ambiguous given that an alignment is an inference of homology; we may or may not have a good idea of which sites are homologous in any given sequence set. Alignment algorithms compute alignment scores by assigning certain values to matches, mismatches, insertions/deletions, and... | biostars | {"uid": 114570, "view_count": 4163, "vote_count": 3} |
I want to compare two bam files to see whether they are same, how many reads they overlapped, and how many reads are unique. bam1 file was got several years ago and then I convert it to bam1_r1_fq and bam1_r2_fq and then remap to the new reference genome and got new sam file. Then I sorted, added header etc and got the... | Since many aligners work in non-deterministic mode the files will not be 100% identical (more so now due to different reference genomes, differences that may be there due to actual alignment logic, if you used different aligners/different versions of the same aligner etc).
It also appears that you are missing the p... | biostars | {"uid": 254790, "view_count": 2174, "vote_count": 1} |
Hi - when using VEP to get allele frequency information for a list of SNPs, I ask for the gnomad_AF column. I have noticed however that around a third of my list return an NA value. How should I intepret this? Is that of all combined frequency consoritums across multiple continents, this SNP has never been seen (i.e. U... | I think it does count as ultra rare if gnomAD doesn't have it. As long as the comparing tool is configured well in comparing multi-allelic sites (as in, you're *sure* the variant is not in gnomAD), it can be labelled ultra-rare. | biostars | {"uid": 308357, "view_count": 2123, "vote_count": 1} |
It might be a very stupid question for many of you but, since it's my first variant calling, I didn't figure it out yet.
I have **mpileup**'ped two bam files from two samples, then I filtered the results with **vcfutils.pl** and called the genotypes with **bcftools** **call**. Now I have a **VCF** file containing w... | I was recently in a very similar situation. I wrote a bash script that finds the "similarity" between two VCF files. Someone might find it useful:
#!/usr/bin/env bash
sort -u <(grep -v '^#' $1 | cut -f1,2,4,5) > a
sort -u <(grep -v '^#' $2 | cut -f1,2,4,5) > b
comm -23 a b > a_only
comm -13... | biostars | {"uid": 224919, "view_count": 16415, "vote_count": 14} |
How to use step by step the software of IPA (Ingenuity Pathway Analysis) to analyze the interaction between these genes:
IL3RA
CD38
CS
MS4A1
GPC2
in the cases of **lymphoma** disease.
Thank you for your enlightenment.
Best regards,
Dito Anurogo
(A Ph.D. student at Taipei Medical University, Taiwan) | There are several youtube videos, manuals and videos on product owner's website. Please consult them. I think they might have training sessions by vendor. Most of these vendors employ application scientists and contact them. | biostars | {"uid": 9521801, "view_count": 471, "vote_count": 1} |
This is a duplicate of:
1. https://www.biostars.org/p/7372/ from 5.4 years ago and
2. https://www.biostars.org/p/65920/ from 3.5 years ago.
Nevertheless, I found the answers on the second post enlightening, and 3.5 years later it seems worthwhile to have an update from the community (and @lh3) on how you deal ... | This is called "variant warehousing" and there are several open source and commercial efforts in various stages:
Golden Helix VSWarehouse
Paradigm4 SciDB
WuXi NextCODE
CMH Variant Warehouse
ViaGenetics Genesis
Curoverse Lightning
Intel GenomicsDB
Cloudera OMICS
| biostars | {"uid": 211076, "view_count": 1444, "vote_count": 1} |
EDIT: SOLUTION
As @rpolicastro said, the problem had to do with the conda channels. The solution for me was:
conda create -n cutadapt -c conda-forge -c bioconda cutadapt python=3.9
ORIGINAL POST
Hello everyone
I'm having trouble installing cutadapt.
I just installed conda and created a new environment for cu... | It could be related to your channels or the solver is having a problem with your specific linux install.
First try ensuring proper channel order when you go to create the environment.
```
conda create -n cutadapt -c conda-forge -c bioconda cutadapt python=3.9
```
If that doesn't work try using the beta libmamba solv... | biostars | {"uid": 9522705, "view_count": 2258, "vote_count": 2} |
Struggling with biostats and association study designs.
I initially wanted to do an association study comparing two populations and seeing which SNPs are significant. For example, I am looking at just variation between centenarians (people who live >100years) and a control group. Should I be including age as a covaria... | <p>I'm a bit self-taught in this but since no-one has answered in 2 days I'll give it a try, others can feel free to chip in.</p>
<p>>Should I be including age as a covariate?</p>
<p>You add covariates when you expect that they have an influence on your phenotype - for example, gender often has an infl... | biostars | {"uid": 156344, "view_count": 9742, "vote_count": 5} |
I have an article in which two types of multiple protein structures docking are described (multiple docking and ensemble docking) but it is not clearly stated how these approaches differ. | Ensemble docking refers to the approach of generating multiple structures of the target molecule using molecular dynamics simulation and study docking to this ensemble of target structures. Multiple docking refers to the breaking down of the target structure into smaller components that are then used for docking in var... | biostars | {"uid": 411268, "view_count": 783, "vote_count": 2} |
<p>I'm using the SRA toolkit to convert some SRA files to Fastq format. I've been looking at the documentation to make sure I'm doing things right, and the word <em>spot</em> keeps coming up. My question is twofold.</p>
<ol>
<li>What is a <em>spot</em> and how does it differ from a read?</li>
<li>Where is this (offici... | This is the description I received from the SRA staff (Adam Stine).
The spot model is Illumina GA centric. The flowcells have the locations where the adapters have stuck them to the glass of the lane. There are X and Y coordinates that identify these 'spots'. As the camera reads the fluorescent flashes during sequenci... | biostars | {"uid": 12047, "view_count": 23288, "vote_count": 23} |
I understand that different Illumina sequencers can output different numbers of reads (i.e. HiSeq instruments can produce 40-400 million reads/lane, whereas MiSeq can produce 5-25 million reads/lane). My question is why? What factors in the Illumina next-generation sequencing technology impact read count outputs from t... | <p>The two factors that limit the amount of data are 1) the maximum cluster density (i.e., number of clones) that can be imaged and resolved by the camera, and 2) the surface area of the flow cell lane that's imaged (MiSeq flow cells are much smaller than HiSeq).</p>
| biostars | {"uid": 167218, "view_count": 2471, "vote_count": 2} |
I would like to use snakemake to analyze my data sets. As I am going to work with different organisms, I would like snakemake to create a folder for each of them when indexing the genome.
let's say I would like to work with human and mouse data.
In my `config.yaml` file I have the following snippet:
organi... | You'd need `wildcards`. https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#wildcards
[~/Data/scratch/tmp/biostar]$ cat wildcards.py
rule:
input: expand("{organisms}/starIndex/", organisms=config['organism'])
rule get_genome:
output: fa = touch('{organism}/{organism}.fa'),
... | biostars | {"uid": 406385, "view_count": 1863, "vote_count": 2} |
<p>Are there any programs available (Python, Perl, whatever), that can take a degenerate nucleotide sequence and translate it into its multiple possible oligos?</p>
<p>Any help would be appreciated.</p>
| Like Pierre said, this is a combinatorial problem that can quickly blow up in your face. However, that aside, it easy to generate all the combinations using a recursion. Here is a compact implementation in Perl:
```
#!/usr/bin/perl -w
# Lookup table of degenerate IUPAC nucleotide codes.
my %deg2nuc = (
"R"... | biostars | {"uid": 6219, "view_count": 9317, "vote_count": 2} |
Hi all,
My question is to find a method to count enhancer RNAs from RNASeq data. Although it may have been asked before, I could not find any post close to mine. I have a couple of fastq files of RNASeq data. I am using TopHat for alignment. When I put my .bam files to IGV, I can visually see some reads in locations w... | You could use bedtools to count number of reads mapping to interest of your region
> intersectBed -wa -wb -s -a bedFile -b BAMFile
Check different parameters
Keep in mind that eRNA are generally not well detected in most RNA-seq samples because of the way how libraries are prepared.
1) As eRNA are generall... | biostars | {"uid": 228128, "view_count": 2976, "vote_count": 1} |
Hello everyone,
I am interested in analyzing some data from TCGA, specifically the LAML project. From there I managed to download the HTSeq counts for the whole cohort, however I would like to map each sample to specific mutations for given set of genes in order to perform DE analysis between pools of samples with t... | I did a lot of the analysis for the TCGA AML paper. The simplest way to pull mutations is to go to the [paper's supplemental site](https://tcga-data.nci.nih.gov/docs/publications/aml_2012/) and pull Supplemental Table 6. Note that the variants are all on build 36, so liftover may be in order if you're working from a n... | biostars | {"uid": 281955, "view_count": 1650, "vote_count": 3} |
Hello,
I've watched a video from YouTube about OMIM. Then I get that OMIM already had more than 3000 disease-associated genes till last year. Now I want to get all of those genes from OMIM to do some experiments.
I think maybe I should use "Gene Map" of OMIM, but I still don't know how to search to get all disease-as... | I endorse the alternative BioMart. I'd perhaps point to another [link][1] as well. The reason for that is due to the fact that there can be a lag between the latest version of the Ensembl database from our main site (as part of our [release cycle][2]) and the version available in Central BioMart. At the moment they are... | biostars | {"uid": 118566, "view_count": 12846, "vote_count": 1} |
Does anyone know of any tools/scripts that would score a MSA in a sliding window manner?
I want to get the average identity across the length of an operon MSA, so I'm looking for something that gives me back a measure of conservation that I can graph.
I found some old threads on BioStars, but a lot of the linked ... | Wrote my own in the end. Uses some bits of code I found online, but a bit more performant.
https://gist.github.com/jrjhealey/130d4efc6260dd76821edc8a41d45b6a | biostars | {"uid": 258014, "view_count": 3582, "vote_count": 1} |
<p>My lab has sequenced an exome using the "Agilent SureSelect All Exon Kits" ( <a href="http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Product&SubPageType=ProductDetail&PageID=3041">http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Product&SubPageType=ProductDetail&PageID... | <p>According to this post <a href="http://www.biostars.org/p/5187">http://www.biostars.org/p/5187</a> , maybe you can find the information in Agilent's Earray <a href="https://earray.chem.agilent.com/earray/">https://earray.chem.agilent.com/earray/</a></p>
| biostars | {"uid": 57675, "view_count": 26988, "vote_count": 4} |
Hi everyone,
I have two unequal data sets.
A data set
V1 V2 V3
6 42721754 42721769
6 42721757 42721772
6 42721760 42721775
6 42721763 42721778
6 42721766 42721781
6 42721769 42721784
6 42721772 42721787
6 42721775 42721790
B data set
V2 ... | Hey, you can try the idea of Rashedul; however, using *BEDTools*, you may encounter issues with the sorting of the regions and also the fact that you implied how the co-ordinates in B can be repeated.
Here is a solution in trusty AWK:
cat A.txt
V1 V2 V3
6 42721754 42721769
6 42721757 42721772
... | biostars | {"uid": 402757, "view_count": 1315, "vote_count": 1} |
HI,
Can someone give a good definition of the difference ?
Thanks
| UCEs are short- and medium-sized stretches of DNA that are identical between different species. They are often non-coding.
Orthology refers always to coding sequences. It requires that function be conserved between different species, but there is no requirement for identical sequence.
While presumably there is a ... | biostars | {"uid": 9517284, "view_count": 435, "vote_count": 2} |
After I got the filtered vcf file of snps with gatk pipeline, I tried to run PCA with gcta.
afterwords, I tried to find the explained variation percentage for each PCs(principal components).
what I'm confused is that the eigenvalue results I get are always the same number as the sample size.
I thought that the amoun... | The principal components are the eigenvectors of the covariance matrix (or correlation, if you scale) of your data. Now, you have two choices: do you want to focus on the covariance between your N samples, or the covariance between your M SNPs? GCTA focuses on the former, whereas you thought it was the latter. GCTA'... | biostars | {"uid": 9487101, "view_count": 978, "vote_count": 1} |
I'm trying the tuxedo protocol as well as analysis using DESeq2, I wanted to see if I can see in the difference of DE genes. DESeq2 uses something called count matrix ,which I generated using both ht-seq and featurecounts .Now I want to know how do I transform those counts to make it usable for DESeq2 analysis
I se... | The output of both HT-seq and featurecounts can *almost* be fed directly in DESeq2.
- **for FeatureCounts :**
Output looks like :
Geneid Chr Start End Strand Length cond1 cond2
SPBC460.05 I 16470 18062 + 1593 1 12 24
SPBC460.02c II;II 8856;9651 9365;9803 -;- 663 329
SPAC212.11 I 1 5662 - 5... | biostars | {"uid": 238253, "view_count": 4478, "vote_count": 2} |
<p>Hi,
I would like to calculate the percent-identity from a CIGAR string from a <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a>/SAM file containing alignments. I want to calculate the PID only for the aligned region, ignoring clipped ends ("H","S"). I can parse the CIGAR in R and get the sums for each lett... | <p>No one seems to have mentioned it, but how about the "NM" tag ("edit distance" in SAM format specification)? I think this is the closest to "mismatches" that can be obtained in a relatively fast way by parsing bam files. One caveat, indels are always going to be a problem when defining identity and I don't know how ... | biostars | {"uid": 16987, "view_count": 14696, "vote_count": 11} |
Hi, first post here.
So I'm trying take the CDS out of various species' orthologous sequences. I'm running on a Linux server, and am mainly aiming to use BioPython or Linux programs for this.
I've run OrthoFinder on 28 species of seaweed, which gave out roughly 10,000 orthogroup sequences fasta files, each of which i... | Here is a Python code that reads one FASTA file and creates multiple FASTA files for each species separately.
from Bio import SeqIO
d = {}
fh = open('OG0000036.fa')
for seq_record in SeqIO.parse(fh, 'fasta'):
species_name = seq_record.id.split('-')[-1]
if species_name not in d:
... | biostars | {"uid": 9486713, "view_count": 2030, "vote_count": 1} |
Dear Friends,
My vcf file has SNPs available for different population(Africa, America, Europe,East Asia and South Asia ). I want to extract the data for Europe and East Asia together . Kindly let me know the possible ways.
Thanks in Advance | You can do this easily using vcftools, GATK tools, plinkseq etc.
you first have to generate a text file with the list of samples that form the population of your choice, let's say "population_of_interest.txt"
Then,
vcf-subset -e -c population_of_interest.txt input.vcf > output.vcf
or
vcftools -... | biostars | {"uid": 292691, "view_count": 4508, "vote_count": 1} |
Hi,
maybe it's a stupid question, but, are gene symbols supposed to be case sensitive or case insensitive?
E.g. GENE1, gene1, GenE1 represent the same gene?
Thanks | <p>It'll depend on the organism. Human genes, for example, are always upper case (e.g., "GENE1"), with the exception of ORFs (e.g., C17orf12, which probably doesn't exist). Mouse genes, on the other hand, have a capitalized first letter and the rest lower case (e.g., "<em>Gene1</em>", which ... | biostars | {"uid": 99083, "view_count": 2203, "vote_count": 2} |
Hi All,
Is it possible to convert a bam index (.bai) to human readable format? I'm asking mostly for learning, I don't plan to do anything special with it.
There is a good description of the bam index in the [sam spec][1] document, session 5.2 but I would like to see a "real" example of an index in plain text.
Thank... | You can write such a tool yourself using R (just as an example):
> x = file('/Users/sdavis2/Downloads/vcfanno_0.0.7_darwin_386/example/ex.bam.bai')
> open(x,'rb')
> readChar(x,4) # Magic number
[1] "BAI\001"
> readBin(x,integer(),size=1,signed=FALSE) # Number of Ref Sequences
[1] 86
A... | biostars | {"uid": 172515, "view_count": 4296, "vote_count": 2} |
Hello,
this is my first post here. I would like to know if there is a way to call IGB (Integrated Genome Browser) through Java. I want to start a specific instance of IGB from a Java application and automatically show some tracks of interest that are on local file. Is this possible? Is there a way to use IGB into a Ja... | Hi,
Thank you for the great question!
Here are some additional possibilities that may be a good fit for what you want to do.
**Option One: Use IGB links (probably the simplest) - port 7085**
One option is to use ports on localhost, as IGB "listens" to port 7085 on localhost and can respond to commands encoded in a ... | biostars | {"uid": 123400, "view_count": 2397, "vote_count": 2} |
Im using this code to make based on log2foldchange and padj value ,im getting the plot but i want those value for my reference how do i extract the same .
alpha <- 0.05 # Threshold on the adjusted p-value
cols <- densCols(res$log2FoldChange, -log10(res$pvalue))
plot(res$log2FoldChange, -log10(res$padj... | **Edit (October 24, 2018):**
This is now a Bioconductor package: https://www.biostars.org/p/335751/
---------------------------------------------
---------------------------
Your code appears to run fine on my DESeq2 results objects:
<a href="https://ibb.co/cdNecb"><img src="https://preview.ibb.co/kckMqw/you... | biostars | {"uid": 282295, "view_count": 47969, "vote_count": 3} |
<p>bgzip files are backward compatible with gzip, but I have issues when using bgzip compressed vcf files with snpeff (java) or perl scripts that uses IO::Uncompress::Gunzip (that I believe it uses zlib under the hood). In both cases the data is decompressed but truncated after a few hundred lines aprox. I could be tot... | <p>Hi. I have just encountered the same problem and it seems there is a pure-Perl solution surrounding this as shown below</p>
<pre>
my $status = gunzip("in.gz" => "out.gz", MultiStream => 1)
or die "gunzip failed: $GunzipError\n";</pre>
<p>It also seems Apache Commons Comp... | biostars | {"uid": 94240, "view_count": 5247, "vote_count": 6} |
Hi all,
Sorry I know that this question has been asked several times, but unfortunately I haven't been able to find the right answer, or didn't understand.
I'm trying to get TMM normalized counts thanks to edgeR.
I understand that I have to compute normalization factors :
dgList <- calcNormFactors(dgLis... | No, CPM and TMM are not exactly the same indeed.
perhaps try this snippet of code:
dgList <- estimateCommonDisp(dgList)
dgList <- estimateTagwiseDisp(dgList)
norm_counts.table <- t(t(dgList$pseudo.counts)*(dgList$samples$norm.factors))
write.table(norm_counts.table, file="./normalizedCounts.txt... | biostars | {"uid": 317701, "view_count": 29756, "vote_count": 10} |
Hello,
I am currently focusing on identifying denovo mutations from my trio data (parents are unaffected and child is affected). I used PhaseByTransmission. However, I found all denovo mutations (child is heterozygous, and both parents are hom. ref) were not phased (i.e. I am getting '/' instead of '|'). Do you think ... | The program is working correctly. Denovo variants can not be phased by transmission because they are not transmitted from the parents (they arise "de novo"). You also can not phase de novo variants using imputation, as imputation also depends on the variant being transmitted from a parent.
To phase de novo variants, y... | biostars | {"uid": 142884, "view_count": 3659, "vote_count": 3} |
We are currently downloading and analyzing multiple large WGS datasets (30-50x) from patients. So far, we downloaded the data of 20 patients from dbGaP/NCBI (tumor and matched normal respectively). More samples are planned to be included. The download itself via prefetch/fasp was relatively fast and smooth but now the ... | The solution we came up was the following: Our file system is simply slow, and there was nothing that could really be done about it. The main bottleneck was reading from the file system, rahter than writing. Fortunately, some of the nodes had local SSDs, which I could use. So loaded the SRAs via prefetch (ascp) to the ... | biostars | {"uid": 260840, "view_count": 2051, "vote_count": 1} |
Dear all,
I have indexed bam file, and I want to print all alignments on chromosome "2" using pysam.
My code is
import pysam
bam = pysam.AlignmentFile("Aligned.sortedByCoord_rep1.out.bam", "rb")
for line in bam.fetch("2"):
print line
What I get is:
D00733:162:CADM2ANXX:2:1311... | Hi, you are not wrong, you are doing it correctly :)
The AlignedSegment object is independent of a SAM-file. The AlignedSegment contains only an index of the chromosomal identifier (tid), and, thus, it does not contain the chromosome number information. It means that the number you see as 18 in the field 3 of the li... | biostars | {"uid": 258006, "view_count": 3220, "vote_count": 2} |
Hello guys
I'm working on Rna SEQ data, and I want to get good conceptual knowledge about the analysis of the process.
I used the tool bowtie for indexing my reference genome and then the rest is according to the TUXEDO pipeline.
I don't understand what exactly, "indexing" of the reference genome is and why i... | Indexing a genome can be explained similar to indexing a book. If you want to know on which page a certain word appears or a chapter begins, it is much more efficient/faster to look it up in a pre-built index than going through every page of the book until you found it. Same goes for alignments. Indices allow the align... | biostars | {"uid": 212594, "view_count": 26936, "vote_count": 6} |
Dear all,
I have paired-end fastq data generated with Illumina bcl2fastqv2.19 & sequenced on a Novaseq.The i5index is 7bp long, the i7 8bp long
R1.fastq.gz contains R1 101bp reads:
@A00154:125:HGKTMDMXX:1:1101:10420:1000 1:N:0:AACTGAGG+ATGCGTC
CTGGCCGTCTCAGCCGAGAAGCCGAGGATTGAATGGGCATGGAGACTGAACTACCCC... | An `awk` solution:
$ awk -v FS="\t" -v OFS="\t" 'NR==FNR {split($1, id, " "); umi[id[1]]=$2; next;} {split($1, id, " "); $1=id[1]":"umi[id[1]]" "id[2]; print $0}' <(zcat R2.fastq.gz|paste - - - -) <(zcat R1.fastq.gz|paste - - - -)|tr "\t" "\n"|bgzip -c > R1_umi.fastq.gz
$ awk -v FS="\t" -v OFS="\t" 'NR=... | biostars | {"uid": 357359, "view_count": 6501, "vote_count": 1} |
Hello everyone,
I know that affymetrix probeset ids are portable across platforms: the same probeset id `1090_f_at` always refers the same gene (probe set). Is it the same for probe ids?
Executing, as discussed in the "affy" package vignette, the code:
> pm(Dilution, "1090_f_at")
on the chip HG_U95Av2, for the ... | It may depend on the source of the file you are using to obtain probe ids. Probe IDs in files from Affymetrix are integers and are associated with a specific feature (x, y position) on the microarray. For clarity this is different than a probeset id. A probeset id refers to a collection of probes (you seem to know this... | biostars | {"uid": 176790, "view_count": 2627, "vote_count": 1} |
Hi,
I'm working on bacterial sulfur metabolism and I would like to be able to extract as much information as I can from the different pathways linked to this metabolism (at least all the biochemical reactions and the enzymes that catalyze these reactions and if possible, the genes coding for these enzymes). Here is... | Try this just using paxtoolsr with the BioPAX Level 3 file you have:
# Update paxtoolsr
First, update to the paxtoolsr development version (I just updated a few things):
setRepositories(ind=1:6)
options(repos="http://cran.rstudio.com/")
if(!require(devtools)) { install.packages("devtools") }
... | biostars | {"uid": 221424, "view_count": 2249, "vote_count": 2} |
**Edit 1:** The following is Y/Auto depth versus age in a cohort. Individuals in this cohort are not known to be cancer patients.
![enter image description here][1]
**Original question:**
In WGS/WES studies I read and studies I participated in analyzing, I notice that the average sequencing depth on Y chromosome var... | Hi Samuel,
I would guess it is the age related "Loss of the Y chromosome" you see in the data, which is a known effect.
See:
[Loss of Chromosome Y and Its Potential Applications as Biomarker in Health and Forensic Sciences][1]
for example.
"Loss of chromosome Y (LOY) is a mosaic aneuploidy that can be detected... | biostars | {"uid": 9482437, "view_count": 1667, "vote_count": 3} |
<p>Dear everyone,</p>
<p>I have been asked to comment on an experiment design that involves WES or WGS of cancer cell lines which lack matched normal.</p>
<p>I know that this design is far from ideal, but I was wondering if there are people who have already stream-lined it (to the extent possible of course). I ca... | <p>The bottom line is that without a matched normal, you're just not going to be able to call the somatic status for the vast majority of sites. That said, you can winnow down a list to those you *suspect* are somatic. Some ideas:</p>
<ul>
<li>Weed out sites with high frequency in the population</li>
<li>If ... | biostars | {"uid": 97834, "view_count": 5527, "vote_count": 5} |
I was checking some of the variants I have found in cancer samples that I have been analysing. I am not much aware of how COSMIC data should be interpreted. So if something is already found in COSMIC, can we consider that variant novel or something significantly important for publication? | COSMIC does provide a large catalogue of somatic variants from many sequencing studies, although their data can be somewhat messy (they include variants sometimes which are not marked as somatic). Examining COSMIC can be reasonably good evidence at determining whether somatic variants have been seen before. That said, ... | biostars | {"uid": 181374, "view_count": 1625, "vote_count": 1} |
I am 34 now. I have no time to prepare for any cet for PhD. I need a PhD for my job and my future.
Please can you help me how to do PhD in bioinformatics, and where to go for distance education in bioinformatics? | > I am 34 now .i have no time to prepare for any cet for phd
Its never too late. See [this][1]
> ..i need a phd for my job and my future .
No, that cant be true. People have jobs and future even without a PhD.
> please can help me how to do phd in bioinformatics ,and where to go
> for distance educatio... | biostars | {"uid": 306026, "view_count": 3236, "vote_count": 2} |
The invocation of [VarDictJava][1] in paired variant calling mode is
VarDict -b "/path/to/tumor.bam|/path/to/normal.bam"
Now obviously in my CWL I would like the tumour and normal BAM to be separate inputs. However, I'm not sure how to combine these into a single command line argument in the actual CommandLi... | Hello @ttmigueltt,
Here's an alternative solution if you will always have both samples; no `InlineJavascriptRequirement` needed:
cwlVersion: v1.0
class: CommandLineTool
inputs:
normal:
type: File
format: edam:format_2572
tumor
type: File
format... | biostars | {"uid": 317087, "view_count": 1858, "vote_count": 1} |
<p>When trying to investigate a 16S rRNA dataset, I often identify several dozen/hundred species/families which are found in higher/lower abundances. I then start doing literature searches to see what they could be doing, where they have been observed before etc. </p>
<p>To me this sounds:</p>
<ol>
<li>Really selecti... | <p>On following Neil's advice, and reading some papers I reverted back to <a href='http://img.jgi.doe.gov/cgi-bin/w/main.cgi'>IMG</a> to see what meta-data they collect with their published genomes, and actually, it's quite substantive.</p>
<p>On clicking into the 'Genome Browser' section you get presented with a list... | biostars | {"uid": 77151, "view_count": 3829, "vote_count": 3} |
Dear lazyweb, here is the new menu for `samtools index`:
```
Usage: samtools index [-bc] [-m INT] [out.index]
Options:
-b Generate BAI-format index for BAM files [default]
-c Generate CSI-format index for BAM files
-m INT Set minimum interval size for CSI indices to 2^INT [14]
```
What is the **C... | It depends on how long your contigs/chromosomes are. The biggest benefit to CSI is that it supports indexing BAM files with contigs longer than 2^29-1 bases. At least in plants this isn't an uncommon requirement. | biostars | {"uid": 111984, "view_count": 9824, "vote_count": 3} |
As the title says, I'm working on variant calling for somatic variant discovery where I have tumour samples, but no normal samples to compare with.
Previously I've been using GATK's UnifiedGenotyper for variant calling, but as this tool is deprecated, I want to switch to the newer GATK variant calling tools. However... | Some resources that address your question more broadly:
- Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data: https://www.nature.com/articles/srep43169
- https://www.biostars.org/p/207536/
| biostars | {"uid": 283279, "view_count": 6291, "vote_count": 2} |
Hi all,
Can someone help me understand the RSeQC Output from infer_experiment.py?
So this is the output:
This is PairEnd Data
Fraction of reads failed to determine: 0.0560
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0192
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9247
So... | It means you have a standard (dUTP-based) strand-specific library. If you want to use featureCounts, you'll want the `-s 2` setting. For HTSeq-count it's `--strand reverse`. | biostars | {"uid": 295344, "view_count": 7312, "vote_count": 7} |
I have bam files that I have split into unmapped, uniquely mapped and multimapped bam files from HISAT2 alignment. I am trying to merge the sorted unmapped and uniquely mapped bam files with the command
samtools merge A1_merged.bam -b A1_unmapped.bam A1_unique.bam
and am getting an error
[E::hts_open_f... | -b FILE List of input BAM filenames, one per line [null]
`-b` would be necessary if the file names were in a separate text file.
It is simply
samtools merge A1_merged.bam A1_unmapped.bam A1_unique.bam
| biostars | {"uid": 442691, "view_count": 2279, "vote_count": 1} |
I did:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq")
I got the output and the installation
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.6.0 (2019-04-26).
Installin... | As the error message states, you're missing the package `xml2-config`. You can google how to install that (probably `libxml2-dev`) on your OS (if you're on Ubuntu/macOS, it should be easy with a package manager). | biostars | {"uid": 378437, "view_count": 8722, "vote_count": 2} |
Hello, this is a very basic question but I was wondering if someone could help me understand if I've used the correct GTF file and Fasta file for the mouse genome indexing. I got the relevant Fasta file and GTF file from ensembl:
GTF:ftp.ensembl.org/pub/release-103/gtf/mus_musculus/Mus_musculus.GRCm39.103.gtf.gz
Fasta:... | The genome construction step line looks good. Also consider including the `--sjdbOverhang` parameter. While the default value of 99 is usually fine, as stated in STAR's manual this should be chosen according to your maximum read length in the dataset by subtracting 1. So, if you have 100 nt reads, `--sjdbOverhang 99` i... | biostars | {"uid": 9465434, "view_count": 3818, "vote_count": 4} |
<p>Which version control system do you prefer to use in your projects and which one is more commonly used. I tried using SVN and CVS but never got the hang of them. I currently use git for most of my projects. Which one is more common among bioinformaticians?</p>
| <p>Having made the progression from CVS to SVN to git, I have to say I prefer the latter, although it's taken me a while to wrap my head around it where I always felt quite comfortable with CVS/SVN. Using <a href="http://github.com">github</a> has helped a lot, but as I found out yesterday the web based merging tools ... | biostars | {"uid": 14896, "view_count": 2983, "vote_count": 6} |
I work with RNA-seq data and have found a few deferentially expressed genes across particular tissue sample. Now I have been instructed to work with GTEX data to see the deferentially expressed genes across different tissue samples.
Now to go green with GTEX data set, I first don't understand their sample codes like
... | In [the download section][1], where it says "A de-identified, open access version of the sample annotations available in dbGaP.", you should find a file called `GTEx_Data_V4_Annotations_SampleAttributesDS.txt`, containing the annotation of each sample. For example GTEX-N7MS-0007-SM-2D7W1 is from Whole Blood.
[1]: htt... | biostars | {"uid": 149012, "view_count": 9081, "vote_count": 3} |
I am trying to do some exploratory bioinformatics on TCGA data using fgsea.
Our lab looks at a specific gene so I was trying to see whether high levels of this gene in TCGA expression data is correlated with enrichment of any genesets. I have been preranking the data using DeSeq2 (and using the F stat as a ranking) ... | Personally, I think the low/high stratification isn't ideal because you lose information about the expression of your gene of interest (you're collapsing everything into two values: low or high). I prefer the continuous design (edit: however, please see discussion below; important caveats).
An alternate approach wou... | biostars | {"uid": 443094, "view_count": 2388, "vote_count": 1} |
Dear All,
I'm trying to download wgEncodeCrgMapabilityAlign100mer.bigWig for human genome 38.
I can get the same file for hg19 from the golden path `ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/`
I can not find such a file in the hg28 directory
`ftp://hgdownload.soe.ucsc.edu/g... | http://hgdownload.soe.ucsc.edu/gbdb/hg38/hoffmanMappability/ ? | biostars | {"uid": 487547, "view_count": 1850, "vote_count": 1} |
<!-- language-all: lang-r -->
Hi,
I may have missed something but,
I have 2 ranges objects like this:
suppressPackageStartupMessages(library(GenomicRanges))
#> Warning: package 'S4Vectors' was built under R version 3.5.1
rg1 = GenomicRanges::GRanges(seqnames = c(1,1,2),
... | <!-- language-all: lang-r -->
Just found that I should be able to do it with the `pintersect`
function from a Pair object. In my example
it works but I am not familiar with this method so I am not sure if it would
be general enough.
suppressPackageStartupMessages(library(GenomicRanges))
#> Warning: pa... | biostars | {"uid": 371231, "view_count": 1227, "vote_count": 1} |
Hi
Can we sort BAM files according to the read name? As the normal sorting happens on the co-ordinates, can anyone tell how to sort a BAM file on read names? I am trying to run HT-Seq count on paired end SAM files but receiving warnings for which I have to sort the BAM in read names and then create its SAM and then r... | pass the `-n` flag to [samtools][1]
samtools sort -n inputfile output
http://samtools.sourceforge.net/samtools.shtml
[1]: http://samtools.sourceforge.net/ | biostars | {"uid": 78318, "view_count": 21941, "vote_count": 3} |
How to merge unique/non overlapping genes between 2 gene model GFF3 files?
I have 2 gene models:
1. Recent supposedly higher quality gene model
2. Older supposedly lower quality gene model
Some genes though that are described in literature have been removed in the more recent gene model. While they are in ... | `bedtools intersect -v` is one option for identifying the unique genes from the older gene model. <https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html> | biostars | {"uid": 9553217, "view_count": 444, "vote_count": 1} |
Hello Everyone,
I have a VCF with multiple individuals from multiple populations and I would like to get a summary of the allele frequency spectrum for each population. I know that VCFtools has some nice options for outputting allele frequencies. However my data is from non-model organisms and I think using the refere... | This can easily be accomplished via [VCFlib](https://github.com/ekg/vcflib)
If the end goal is association testing have a look at GPAT: https://github.com/jewmanchue/vcflib/wiki
**EDIT**:
**GPAT++** now supports population summary statistics: https://github.com/jewmanchue/vcflib/wiki/Basic-population-statistic... | biostars | {"uid": 101218, "view_count": 8396, "vote_count": 4} |
I want to store a docker image with the input data, code, software, intermediate results and results. This will be a massive file.
Is there something like the sequence archive for people who want to upload a docker image of their whole study? If not, what is the best/cheapest way to store such a file?
Any relate... | I get the point of using a Docker image is for reproducibility, but the key selling point of Docker is it's modularity! It seems slightly blasphemous to put *everything* onto a Docker image. Why not just a VM image if you're going to make an offline reproducibility archive of multi-gigabytes?
Instead I would give so... | biostars | {"uid": 206026, "view_count": 1988, "vote_count": 5} |
I have a big data matrix and each column has named with multiple information and separated by an underscore.
For an example; Genotype_Time_Replicate: X_T0_1, X_T0_2 etc
I want to average my data for downstream analysis.
How can I average replications (**Case 1: in column data**), and averaging repeated raw dat... | Assumption is that average is applied for every 3 columns and updated with data frame df1 from OP:
results=data.frame(apply(array(as.matrix(df1[,-1]), c(nrow(df1),3, ncol(df1)/3)),3, rowMeans))
results=cbind(df1$Gene, results)
results
df1$Gene X1 X2 X3 X4 X5 ... | biostars | {"uid": 318210, "view_count": 11837, "vote_count": 2} |
Hi,
I have got my first Nanopore sequencing data and the first step was to see if the data is good. Has anyone has any experience with this kind of data and can tell me how to interpret the results.
The whole report can be downloaded [here][1] (not sure how to post it here). Allin all it looks quite good to me, but ... | a few of your reads are very long and those skew and alter the plots.
there is also no binning for the first 10 bases then it is binning into huge bins subsequently, again makes the plot misleading
do not remove the beginning of the reads for QC reasons, that is rarely an advisable course of action.
I would filter t... | biostars | {"uid": 9521828, "view_count": 1092, "vote_count": 1} |
I am using esearch query as `$query = "SS1G_03709+AND+gene[filter]";`, but it gives me all (gene+ mRNA+genome sequences). What filter do I need to use so I only get gene sequences in my search? I tried a few filters from [here][1], but couldn't find anything to limit my search for genes.
[1]: https://www.ncbi.nl... | One way (sequence truncated for brevity):
$ esearch -db nuccore -query "SS1G_01676 [GENE]" | efetch -format fasta | grep ">" | grep -v "genome" | awk '{print $1}' | epost -db nuccore | efetch -format fasta
>XM_001597432.1 Sclerotinia sclerotiorum 1980 UF-70 hypothetical protein partial mRNA
ATGGCGCCCA... | biostars | {"uid": 345772, "view_count": 3271, "vote_count": 2} |
<p>Hi, everyone:</p>
<p>I found that there was no golden standard method for single cell RNA-seq subgroup. There were many papers showed different methods for this analysis. Now I wanna try these different clustering methods to my data. How to evaluate them using R, python, etc. I don't want to do biological exp... | <p>There is no standard method for evaluating clustering methods other than comparing to some ground truth when it is available. There are however several measures of clustering "quality" e.g. the silhouette (in R <a href="https://stat.ethz.ch/R-manual/R-devel/library/cluster/html/silhouette.html" target="_bl... | biostars | {"uid": 160958, "view_count": 2041, "vote_count": 2} |
Hey I have a fasta file which contains more than 80 sequences. I want to take each sequences in different files and the file name should be header of corresponding sequence. | curl https://raw.githubusercontent.com/gouthamatla/fasta_File_Manipulation/master/SplitFastaFile.py | python - <in.fasta> | biostars | {"uid": 170646, "view_count": 2763, "vote_count": 1} |
<p>Hey guys!</p>
<p>Just a newbie in bioinformatics. I have a problem about integrative bioinformatics: how to combine those database to make my queries more efficiency?</p>
<p>Is there any browser or interface which can help me to search multiple databases while only input one query?</p>
| <p>As Sean said, there is no such magic box for all queries for all databases, nevertheless you could have a look at <a href='http://bio2rdf.org/'>bio2rdf</a> to get an idea of what is a Integrative database.</p>
<blockquote>
<p><a href='http://www.ncbi.nlm.nih.gov/pubmed/18472304'>http://www.ncbi.nlm.nih.gov/pubme... | biostars | {"uid": 74565, "view_count": 3390, "vote_count": 1} |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.