INSTRUCTION stringlengths 48 14.1k | RESPONSE stringlengths 14 8.79k | SOURCE stringclasses 1
value | METADATA stringlengths 48 55 |
|---|---|---|---|
Hi,
I was wondering which NCBI reference genome assembly to use for mouse GRCm38, if I don't want to use the UCSC mm10. I thought the FTP-site of the Sanger mouse genomes project might be a good place to check: ftp://ftp-mouse.sanger.ac.uk/ref/ Does anyone know what the 68 refers to in the file name - [GRCm38_68.fa][1... | <p>This is one, but from ensembl --> ftp://ftp.ensembl.org/pub/release-68/fasta/mus_musculus/dna/. Inappropriate?<br />
<br />
This Ensembl version (release 68) corresponds to GRCm38 (mm10) (https://www.biostars.org/p/52254/)<br />
<br />
Some sorces to download mm10 genome version:<br />
http://hgdownload-test... | biostars | {"uid": 146780, "view_count": 13878, "vote_count": 1} |
<p>I received genome-wide association (GWAS) data from a colleague who's supposedly done all the imputation and quality control according to the consortium's standards. Genotyping was Illumina 660, imputed to HapMap (3.2 million SNPs total).</p>
<p>The data came to me as a matrix of 11,000 samples (rows) and 3.2 milli... | <p>For imputation, the primary QC really should be done on the input genotypes, rather than directly on the imputations. Prior to imputation, I remove SNPs at MAF < 0.01, HWE < 1e-06, and only used SNPs present on 97% of the samples. Also, since Illumina data has relatively few A/T and G/C SNPs, I also remove th... | biostars | {"uid": 6476, "view_count": 40814, "vote_count": 30} |
Hi,
I keep coming up against these problem when writing scripts using BioPython SeqIO..
The first, is I can't find in the documentation of BioPython (or the cookbook) how to change a SeqcRecord attribute.. e.g. add a number to a `record.id` (or `record.name`) to give it a unique identifier (a common problem in prepar... | I have a feeling there's a minor confusion with ID and name in your example - you can use the print function to see all attributes of a SeqRecord, here for a small test record:
for s in SeqIO.parse('./test.fasta', 'fasta'):
print(s)
prints
ID: Unchanged
Name: Unchanged
Description: ... | biostars | {"uid": 103663, "view_count": 6604, "vote_count": 1} |
I am new to analysing ATAC-seq data.
As mentioned on https://www.biostars.org/p/209592/, there seem to be two ways to use MACS to analyse ATAC-seq data.
1. Utilising the --shift -100 --extsize 200 command
This, I believe, is to find where the cutting sites are.
2. Utilising the --shift 37 --extsize 73 com... | You can use MACS, but it is not the best tool for identifying open chromatin regions. I would recommend using Fseq: http://fureylab.web.unc.edu/software/fseq/ It was designed to analyze DNase -seq data, the predecessor of ATAC-seq. When analyzing data from either experiment, you do not really want to look for overl... | biostars | {"uid": 324287, "view_count": 3791, "vote_count": 1} |
Hi,
By default IGV indicates insertions with respect to the reference with a purple I, and I would like to hide it or change the color, I have read the manual and it is making me crazy, I can´t find the way to do it, somebody knows if it is possible? | Preferences -> Alignments -> Hide indels < 'x' bases (?) | biostars | {"uid": 339007, "view_count": 2070, "vote_count": 1} |
Hi,
I am trying to compare few models for evoultionary distance calculation. I want to compare just those basic ones - Jukes-Cantor, K2P, Tamura, Tamura-Nei, HKY(Hasegawa-Kishino-Yano), GTR (general time reversible = Tavare) and Falsenstein81. I have already found equations for evolutionary distance calculations for f... | I would first look at the original papers for the different models, you will find the equations for sure. I know that the APE/phangorm package uses those but I think they merely call [phyml][1]. I looked briefly and you can request the source code and that will give you some code to work with.
[1]: http://www.atgc-mo... | biostars | {"uid": 136434, "view_count": 4204, "vote_count": 2} |
I very much like the IGB tools and its features. While I have been able to make a good use of it, I have been facing a problem and can't seem to find a solution how much I try. I am trying to view the aligned tophat output (mapped.bam and junction files from aligned RNAseq data on the reference *A. lyrata* genome. When... | Hello,
It sounds to me like the reference genome you used for the alignment step is using different names for scaffolds than the version of the sequence IGB is using.
**Some useful info**:
IGB is getting reference genome sequence and gene model annotations from a publicly accessible IGB QuickLoad site located at:
h... | biostars | {"uid": 147826, "view_count": 4013, "vote_count": 3} |
Hi guys,
I've to create a variable a in which elements are column names of a database.
For example, I have the following column names of a df:
colnames(df)
"PS_01", "PS_01_mod2", "PS_02", "PS_02_mod2"
I want to create a vector a in which elements are the column names of df ending with mod2, so I wa... | Hi, a simple `grep()` command will do this for you, and we can add a regular expression ('regex') to ensure positional specificity:
vector <- c('PS_01', 'PS_01_mod2', 'PS_02', 'PS_02_mod2', 'mod2_mod1')
idx <- grep('mod2$', vector)
vector[idx]
[1] "PS_01_mod2" "PS_02_mod2"
The dollar, `$`, means that ... | biostars | {"uid": 9476797, "view_count": 577, "vote_count": 1} |
Hi!
I have an alignment (.bam) of reads to mm9 genome. I sorted it with `samtools sort`, so that later I can use `-sorted` key with bedtools. I also created a .bed-file with regions of interest, in which I want to count number of reads, that mapped to them. I tried this: converted .bam to .bed with `bedtools bamtobed`... | By default, the `-sorted` option assumes that both of your input files have chromosomes sorted lexicographically (chr1, chr10, chr11, etc.). I suspect one of your files is this way and one is not. Alternatively, if you want to use a different order, you can use the `-g` option. See the docs for details: http://bedtools... | biostars | {"uid": 102074, "view_count": 8544, "vote_count": 1} |
This is a follow-up to an earlier question of mine.
I tried the following command (copied verbatim from [UCSC's mysql access docs][1]):
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A
...but it fails with the error message:
ERROR 1045 (28000): Access denied for user 'genome'@'my.host.redacted' (usin... | OK, problem solved.
**Diagnosis:** <a href="https://en.wiktionary.org/wiki/PEBCAK">PEBKAC</a> [1]
**(one) Solution:** change the command line to
mysql **--no-defaults** --user=genome --host=genome-mysql.cse.ucsc.edu -A
---
[1] More specifically: I had a long-forgotten `~/.my.cnf` file lingering aroun... | biostars | {"uid": 166748, "view_count": 2395, "vote_count": 1} |
Hi all,
I have three somatic variants (mutations) detected in a single tumour sample. They come from Whole Genome Sequencing technologies and to call them normal and tumour samples were compared.
The mutations are supported by the same reads. It's a bit suspicious to me because this could indicate that the reads... | >The mutations are supported by the same reads. It's a bit suspicious to me because this could indicate that the reads are from another part of the genome.
It could also indicate that there are three adjacent mutations, or another sort of mutation. Without additional context, is it difficult to determine whether the... | biostars | {"uid": 254467, "view_count": 2979, "vote_count": 1} |
Hello, I always believed expression matrix on GEO is normalized. However, I get huge big log2FC from [GSE85957](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85957) today.
> head(expr_3)
# A tibble: 6 x 8
SYMBOL logFC AveExpr t P.Value adj.P.Val B ENTREZID
<chr> <dbl> ... | Well, the easiest way is to read the data processing sections for each sample.
> The data were analyzed with Microarray Suite version 5.0 (MAS 5.0)
> using GeneData Expressionist® Pro Refiner. The trimmed mean target
> intensity of each array was arbitrarily set to 100.
The next easiest is to use [GEO's built-i... | biostars | {"uid": 395494, "view_count": 3690, "vote_count": 1} |
I've got a new issue...
I would like to compute the average distance between two distinct motifs in the same sequences list than before. Have you some clue on how manage this ???
I just come to do it for one motif like that :
source("motifOccurrence.R")
motif <- c("T", "C", "A", "A")
motid... | Assuming I understood your problem this is my attempt to a solution. I do not use the functions in the script you pointed out, but the `Biostrings` Bioconductor package. Also, I use the Bioconductor package `BSgenome.Scerevisiae.UCSC.sacCer3` for the yeast genome as example sequence data.
# load required packag... | biostars | {"uid": 216202, "view_count": 2726, "vote_count": 2} |
I'm curious as to why I'm getting two different values with bedtools intersect with two sorted bedfiles:
bedtools intersect -u -a test1.bed -b test2.bed | wc -l
This gives me 157,273
However, when swapping -a and -b:
bedtools intersect -u -a test2.bed -b test1.bed | wc -l
This gives me 158,095 | This is normal that order affect the result. Read carfully the help [https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html][1]
First you report all sequence from A that overlap B
And secondly you report all sequence B that overlap A
The only case where both will give you the same result it is if ... | biostars | {"uid": 9473825, "view_count": 618, "vote_count": 1} |
<p>I'm trying to find all the reads (by name) from a BAM file that align to various regions in a bed file. Right now I can do this with <code>bedtools</code> using <code>intersectBed</code>:</p>
<pre><code>intersectBed -abam reads.bam -wo -f 1 -b regions.bed -bed
</code></pre>
<p>From this one can parse all the read ... | The BEDOPS <a href="http://code.google.com/p/bedops/wiki/bedmap">`bedmap` tool</a> with the `--echo`, `--echo-map-id`, `--delim` and `--multidelim` options can also answer this very quickly. You can pipe in reads into `bedmap` by using the <a href="http://code.google.com/p/bedops/wiki/bam2bed">`bam2bed` script</a>:
... | biostars | {"uid": 61044, "view_count": 4345, "vote_count": 1} |
Hello all, I am new in plink analysis
I have Map file and I know that location (start /end) of ***CD2AP ***gene on chromosome 6 has base pairs 47,477,745 to 47,627,262
How can I use physical position column in MAP file to extract SNPs of this gene
Any help will be appreciated | Dear,
First you need to make sure which transcript you are interested. Keep in mind that the same SNP will have different cDNA coordinates between transcripts. Also you need to watch out for the genome version. Because g coordinates will also vary between different genome versions. Moving from your example, you can ... | biostars | {"uid": 167027, "view_count": 3776, "vote_count": 1} |
<p>I'm new in this field. I want to identify circular RNAs from RNA-seq. I want to know which tools I could choose to detect circular RNAs using some simple commands. Thanks!</p>
| You could try [CIRCexplorer][1], a combined strategy to identify junction reads from back spliced exons and intron lariats using TopHat and TopHat-Fusion. The commands are very simple. For more information. please refer to [**Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147**... | biostars | {"uid": 127785, "view_count": 11857, "vote_count": 8} |
Hi,
I am using edgeR to carry out DE analysis for my RNA Seq samples, may I know how can I construct the design matrix and how can I make sure that during testing, the DE genes shown are of the correct contrast?
My current steps are shown below:
**Current data type:
subject: 1,2,3,4**
**treatment for each ... | Please see section 3.4.2 of the edgeR vignette.
result_glm <- glmQLFTest(fit, coef=5) # Or maybe coef=4, it'll be the last column in "design" | biostars | {"uid": 278093, "view_count": 4668, "vote_count": 1} |
Hello,
I was wondering if there is a website in which I can retrieve the list of genes for each ontology.
For example for the biological process "Regulation of Gene Expression," I would like to have all the list that belong to this ontology etc..
Thanks in advance | I recently wrote a small tool to fetch all the children of a given term in GO: http://lindenb.github.io/jvarkit/GoUtils.html
there is an example to fetch all the associated genes:
Use GO annotation to retrieve genes associated to GO:0005216 ‘ion channel activity’
join -t $'\t' -1 1 -2 2 \
<(java -jar... | biostars | {"uid": 319749, "view_count": 1085, "vote_count": 2} |
I've ran a BLAST using the Sol genomics network database for my tomato transcriptome
http://solgenomics.net/
I have my transcriptome labeled with the sol gene IDs, but need to convert them to a more typical gene ID such as NCBI-geneID. Any thoughts on how to do this? I've tried using a series of different GeneID conv... | Okay, so I finally completed this task by doing the following:
I contacted the Boyce Thompson Institute who ran the Sol Genomics website to see if they had any conversion sheets from their Sol genomics IDs to something more common. They sent me a very good conversion sheet of Sol gene IDs to UniProt IDs.
If someone k... | biostars | {"uid": 150062, "view_count": 9879, "vote_count": 1} |
Hi:
I have a BED file with sites of a transcription factor binding sites (mm9). I want to annotate these sites, typically located between intergenic regions, to a gene nearby. I checked a publication (PMC3080774) and it lists some tools that can map and annotate.
I tried using Chipseqanno. Initially it was straigh... | You can just use *GenomicRanges* with your peaks BED file and your annotation GFF (after they have both been converted to *GenomicRanges* objects. There is a parameter in the GenomicRanges `findOverlaps()` function called `maxgap`, which would allow you to set your distances of 1kb, 2kb, etc.
With regard to why one ... | biostars | {"uid": 322218, "view_count": 1730, "vote_count": 1} |
Hello,
I want to extract some specific strings in csv file, using either excel, R or Python.
for example as below: I want to find string from column A in column B and return in column C with 5 amino acid before and after **N**; thanks!!
```
A B C
INETTD... | Using R:
getPreceding <- function(A, B, N = 4) {
x <- regexpr(A, B)
substring(B, x - N, x + attr(x, "match.length") - 1)
}
A = "INETTDFR"
B = "...IGASAFYKGYESIVGKINETTDFRSTRDAQGHGTHTAST..."
getPreceding(A, B)
# [1] "IVGKINETTDFR"
| biostars | {"uid": 109077, "view_count": 4342, "vote_count": 1} |
I've installed BLAST and BLAT on my computer (OSX) but am confused with how many different files there are to download to set up a database on my computer and how to go about it. Can I use one with both BLAST and BLAT? Should I get the partially non-redundant database? | Once you have installed `blat`, you can download a FASTA file for your genome of interest from UCSC. If you wanted `hg38`, for instance:
$ for chr in `seq 1 22` X Y; do echo $chr; wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg38/chromosomes/chr$chr.fa.gz | gunzip -c - >> hg38.fa; done
You can use this... | biostars | {"uid": 261970, "view_count": 2163, "vote_count": 1} |
I have an assembled transcriptome that I blasted against the nr_db from NCBI. I want to use MEGAN to get some taxonomic information on the reads. I imported my blast xml files into MEGAN5 and all seemed to work fine. When I click a node to inspect which hits are associated with a given taxon I encounter a problem. The ... | I figure out what went wrong. It was a tiny formatting error in my blast input files that corrupted everything, thought blast had no problem with it. Fixed it and now everything is working fine! | biostars | {"uid": 152206, "view_count": 1952, "vote_count": 1} |
Can I index a BAM file that is sorted by queryname instead of coordinates using samtools? | no, indexing is only for **coordinate** | biostars | {"uid": 258116, "view_count": 2004, "vote_count": 2} |
Hello Biostars Community,
General question(s) here, specifically in regards to sequencing platforms and some related questions on sequencing, as well?
1. Could using a newer/the newest computational genome/annotation (for example, presently, Ensembl 107 or the newest Gencode version) adversely effect the actual t... | Excellent responses by GenoMax to wonderful questions by Pratik. I echo what GenoMax says.
IMHO, the platforms ar einherent to capture technologies as well. NOT necessarily or everytime one would intend to use the same samples with different sequencing platforms/technologies unless the lab is rich. Even otherwis... | biostars | {"uid": 9539218, "view_count": 505, "vote_count": 2} |
What are currently the best tools for lifting over genome coordinates from one custom genome build to another custom genome build.
I found this 4 year old post that mentions **UCSC liftOver** as the top tool but that seems to be limited to model organisms as you need the chain file from UCSC . I can't find anywhe... | As mentioned elsewhere, our https://github.com/wurmlab/flo tool can do a decent chunk of the job | biostars | {"uid": 226368, "view_count": 3963, "vote_count": 1} |
<p>When I try this [vcftools_results]$ /home/X/vcftools_0.1.6/perl/vcf-validator sample1.flt.vcf.gz</p>
<p>it gives an error.</p>
<p>Can't locate Vcf.pm in @INC (@INC contains: /share/lib64/perl5/5.8.8 /share/lib64/perl5 /share/lib/perl5/5.10.0/x86_64-linux-thread-multi-ld /share/lib/perl5/5.10.0 </p>
<p>/share/lib/... | <p>Hi Deniz</p>
<p>Have you set the environment variable PERL5LIB as it is defined in <a href="http://vcftools.sourceforge.net/docs.html#install">VCF Tools installation</a> ?</p>
<p>It is as simple as calling:</p>
<pre><code>export PERL5LIB=/path/to/your/installation/perl
</code></pre>
<p>Regards.</p>
| biostars | {"uid": 15163, "view_count": 32227, "vote_count": 7} |
Hi,
I am attempting to make some heat maps with some RNA-Seq data. I used Salmon for my quantification and followed [this][1] link to import my data into R so I can use Deseq2. So I am just going through the Deseq2 little tutorial [here][2]. I am trying to follow their instruction on how to create some heat maps. I ... | You can just do this:
cdata <- colData(dds)
pheatmap(assay(ntd),
cluster_rows = FALSE,
show_rownames = FALSE,
cluster_cols = FALSE,
annotation_col = as.data.frame(cdata))
...or:
pheatmap(assay(ntd),
cluster_rows = FALSE,
show_rownames = FALSE... | biostars | {"uid": 332532, "view_count": 5235, "vote_count": 2} |
<p>My lab has started using the <a href='http://www.halogenomics.com/haloplex/how-it-works'>Haloplex technology</a> to capture the regions of interest.</p>
<p>With this technology most of the reads have the same start/end (I've found that removing the duplicates would reduce the coverage to ~1 base). The reads are gro... | <p>In general, any capture-based technology will have bias. In your case, you're worried that the the bias will be amplified in the detection step.</p>
<p>I would use as many methods as possible to call these alleles, and see what the differences are. With coverage this high, there should be little variation in resu... | biostars | {"uid": 60433, "view_count": 5209, "vote_count": 4} |
I am looking for any two strains of S. pneumoniae for which I can find their raw output sequencer data in FASTQ format and for which I can find their reference genomes (since I plan to align the raw data in the FASTQ format to the reference genomes using Bowtie 2). I know that I could make artificial FASTQ files using ... | You can get FASTQ and FASTA [here][1].
Most strains will provide the raw data associated with the study. For example: http://www.ebi.ac.uk/ena/data/view/ERP000241
[1]: http://www.ebi.ac.uk/ena/data/search?query=streptococcus%20pneumoniae | biostars | {"uid": 105527, "view_count": 2303, "vote_count": 2} |
<p>I should start by saying I have solved this problem, but I feel like my code is ugly and overkill.</p>
<p>I am trying to sort a dataframe on a column containing human chromosomes:</p>
<p>chr1,chr2...chrY, chrX.</p>
<p>the problem is:</p>
<p>chr1, is followed by chr10. </p>
<p>What tricks do you use to deal wit... | <p>Hi Zev, </p>
<p>what you are looking for is: <a href="http://rss.acs.unt.edu/Rdoc/library/gtools/html/mixedsort.html">mixedsort {gtools}</a></p>
<blockquote>
<p>Order or Sort strings with embedded numbers so that the numbers are in the correct order</p>
</blockquote>
<pre><code>package 'gtools' was built under R ver... | biostars | {"uid": 17224, "view_count": 9162, "vote_count": 6} |
I am trying to characterize the depth of coverage for SNPs/INDELs/other variants in my BAM/SAM file. Using samtools mpileup generates a nice VCF that gives me information on this, but it's not quite complete. Entering the "-t AD" flag gives me the depth of the alternate alleles compared to the reference. That is what I... | > It would be straightforward to write an if statement of the kind
> if ALT column is T then return AD and if AD is > 20 return "likely to be target organism strain"
using vcffilterjs https://github.com/lindenb/jvarkit/wiki/VCFFilterJS (will add NOT_TARGET_ORGANISM_STRAIN in the column FILTER)
java -... | biostars | {"uid": 229935, "view_count": 4185, "vote_count": 1} |
I have downloaded GnomAD vcf file and want to calculate the minor allele frequency of each variant in that file. But I am not quite sure how to do that. I have an INFO column which has AC,AF, AN in there. Does AF refers to minor allele frequency for that variant? If not then how can I calculate the minor allele frequen... | Yes AF is the MAF here.
It bears mentioning that sometimes the variant might not necessarily be the less common allele in all populations, and the major allele might even confer something weakly deleterious. But in these two cases, they only saw one individual with this mutation. | biostars | {"uid": 475377, "view_count": 1140, "vote_count": 1} |
I am using tabix to retrieve information in a specific genomic region. need not the hole information but only let say second and the third column.
My file is constructed as follows:
```
##INFO=<ID=GENE,Description="Neighbouring Gene">
##INFO=<ID=A1,Description="Allele 1 (+)">
#SNPID CHROM POS GENE A1 A... | tabix file.tsv.gz chr12:345-678 | grep -v "##" | cut -f 1,2,3,7 | biostars | {"uid": 134808, "view_count": 1919, "vote_count": 1} |
I ran into an unexpected feature of blastn.
After extracting some gene sequences from a genome, creating a blast database and blasting back to the reference, lot of extracted genes are not found in the blast result, while they are certainly there in the genome (as they were extracted from there)
What can be the cause... | After doing some research, I found the answer for my question. The value for `max_target_seqs` is 500 by default.
If raising `max_target_seqs` to some irrationally high value, all genes are shown.
Hence I used
blastn -query GCF_000005845.2_ASM584v2_genomic.fna -db MG1655_genes -outfmt 6 -max_target_seqs 100... | biostars | {"uid": 394390, "view_count": 689, "vote_count": 1} |
Hi,
I analyse micro array datasets to get gene expression data.
I want to filter NCBI datasets by sample type.
For example I want to get only tumor/cancer sample in [GSE19826][1].
I look at all the samples one by one and select them manually.
Is there any simple way or tool to get it or I have to look m... | a simple XSLT generating a shell script from the Sample names:
https://gist.github.com/lindenb/1d23b5d53f1a3694bbd1a7631935140f | biostars | {"uid": 460606, "view_count": 557, "vote_count": 1} |
i am new the area of bioinformatics . Right now working on the tuxedo protocol . Trying to analyze a data based on the e coli reference genome.
this is my file location - **/Desktop/prasanth/TUXEDO/Experiments/Glucose_limited/alignersd/Bowtie/index$ ls
reference_genome.fa**
when i run the command... | Microfuge is right. Your command should be
bowtie2-build -f ~/Desktop/prasanth/TUXEDO/Experiments/Glucose_limited/alignersd/Bowtie/index/reference_genome.fa ~/Desktop/prasanth/TUXEDO/Experiments/Glucose_limited/alignersd/Bowtie/index/reference_genome
Then ~/Desktop/prasanth/TUXEDO/Experiments/Glucose_limited/... | biostars | {"uid": 212140, "view_count": 2051, "vote_count": 1} |
Dear all,
please would you advise, based on your experience, which algorithm is more reliable in confidently calling INDELS in cancer genomes (I am referring especially to INDELS of length > 50bp, let's say 50bp-500bp long).
many thanks,
-- bogdan | pindel can do it but, when you get near to the 500bp mark, are you not then in the realm of small somatic copy number alterations? BBMap can also do this: https://www.biostars.org/p/254305/
In all cases, read length and insert size are obviously key.
Kevin | biostars | {"uid": 304103, "view_count": 1264, "vote_count": 1} |
Hi
I have a folder with 4000 files in it. I would like make a new folder, and copy into it all of the files which contain >50 fasta sequences. How do I do this?
I know that I need to create a simple loop, then grep '>' | wc -l and select only those with >50. But I am new to programming and am unsure how to writ... | Here is how
grep -c '^>' *.fasta | sed 's/:/ /' | awk '$2>50 {print $1}' | xargs mv -t new_folder/
**Update**
grep -c '^>' *.fasta | sed 's/:/ /' | awk '$2>50 {print $1}' | xargs cp new_folder/
P.S: Updated as @[genomax2][1] pointed out.
[1]: https://www.biostars.org/u/18713/ | biostars | {"uid": 196413, "view_count": 2622, "vote_count": 1} |
<p>Hi all,
here are some questions about <strong>paired-end sequencing</strong> for NGS:</p>
<ul>
<li>What are the main differences between <strong>mate-paired</strong> sequencing and <strong>paired-end</strong> sequencing; Should I care when I use tools like 'samtools', maq, etc.... ? Should one, and only one short r... | <p>paired-ends and mate pairs are different protocols. The distance between mate pairs are much longer (2-5kb), while paired-end fragments are rarely more than 500bp apart and can even have <em>negative</em> distance (overlapping pairs)</p>
| biostars | {"uid": 788, "view_count": 34318, "vote_count": 27} |
I want to query the molecular weight of multiple proteins from R given uniprot ids. I thought of using biomaRt or UniProt.ws, but didn't see which field I should query.
There are online tools performing the calculation given a uniprot ID (PIR, ExPASy), but you have to manually enter the input and save the output.
I w... | You can get this information from the [TogoWS REST service][1], starting from UniProt ID. For example, using PROSC_MOUSE (which is the ID, Q9Z2Y8 is the *accession*):
```
library(rjson)
library(RCurl)
u <- getURL("http://togows.dbcls.jp/entry/uniprot/PROSC_MOUSE.json")
j <- fromJSON(u)
j[[1]]$sq$MW
# [1] 30049
```
... | biostars | {"uid": 109706, "view_count": 5368, "vote_count": 2} |
Hi,
I want to extract sequence with header from a fasta file with specific ID given in another file.
As for example:
File: `main.fa`
```
>ADC37925 pep:novel supercontig:GCA_000025145.2:CP001844:1841991:1848551:-1
MNLLKKNKYSIRKYKVGIFSTLIGTVLLLSNPNGAQALTTDNNVQSDTNQATPVNSQDTNVANNRGLANSAQNTPNQSATTNQGIFSTLIGTVLLLSNPNGAQ... | My Solution:
<a href="http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/">UCGS utilities</a>
$ ./faSomeRecords main.fasta id.txt output.fa
option `-exclude` will output sequences not present in "main.fasta" | biostars | {"uid": 127141, "view_count": 18082, "vote_count": 1} |
<p>Is there any way to detect if your rna-seq data is unstranded or stranded</p>
| In case anybody currently looking comes across this post...
The easy-to-use Salmon will check for you as described [here][1]. You can see what the resulting abbreviations correspond to with a nice illustration [here][2].
[1]: https://salmon.readthedocs.io/en/latest/salmon.html#what-s-this-libtype
[2]: htt... | biostars | {"uid": 98756, "view_count": 30700, "vote_count": 18} |
Hi folks. I need to run a de novo short-read genome assembler (on a paired-end/mate-pair library) that prefers outputting shorter but error-free contigs rather than longer contigs/scaffolds which may be mis-assembled. What assembler or what specific setting in an assembler of choice do you recommend to yield such conti... | According to the first GAGE paper, SGA makes shorter, but very much correct contigs. See http://genome.cshlp.org/content/early/2012/01/12/gr.131383.111.full.pdf | biostars | {"uid": 96350, "view_count": 2302, "vote_count": 1} |
Hi everyone,
I've performed ChIP-seq analysis on TFs for a specific cell line for which I only have three histones marks (H3K4me1, H3K27ac and H3K4me3). I used HOMER to annotate differents peak from my datas but now I would like to use these histones marks to improve the annotation (for example if one peak is prese... | It sounds like you're trying to identify 'active enhancers'. There's a couple of interesting options you have to do this. For visualization @Vivek Bhardwaj's answer is great. But i'm assuming that you'd like to have a list of putative 'active enhancers' in which to over-lay your TF ChIP-seq data.
So literature tells... | biostars | {"uid": 186058, "view_count": 4402, "vote_count": 4} |
Hi guys :D
I'm working with distance matrices produced by clustal omega for moderately large fasta files combining sequences of two different plant species in each .
When I was about to finish the script and code the final pipeline step ; which is retrieving the actual sequences corresponding to ID's given in the dis... | So , After looking at the options I have so far from the answers above ... I picked this approach to solve the issue for the reasons listed below and it works very fine for me :D
```
from Bio import SeqIO
from Bio.Alphabet import IUPAC
files=["Left(Aestivum_Japonica).fasta" , "Right(Aestivum_Japonica).fasta"]... | biostars | {"uid": 130294, "view_count": 5487, "vote_count": 1} |
I have a list of protein GI and would like to get accession number of the genome (DBSOURCE in genbank file) using Eutilities.
What would be the easiest way to get genome accession numbers for a list of protein GI? | Here is a perl script to do this. This script is explained in detail [here](http://bioinformatics.cvr.ac.uk/blog/?p=276)
#!/usr/bin/perl
use Bio::DB::EUtilities;
#my @ids = qw(817524604 726965494);
my $infile = $ARGV[0];
my @ids;
open (IN,"$infile")||die "can't open... | biostars | {"uid": 145216, "view_count": 7854, "vote_count": 4} |
<p>I am looking for an antibody database where each antibody is linked with its potential/actual target genes/proteins, <em>i.e.</em> a database similar to <a href="http://drugbank.ca">DrugBank.ca</a> but only for antibodies. It would be really great if the data is in a parse-able format, up-to-date and comprehensive e... | Hi Arman,
Some of them are (Free+ Paid):
- <a href="http://www.antibodyresource.com/antibody-database.html">Antibody Related Databases and Software</a>:
> Antibody related amino acid sequencing tools, nucleotide sequencing tools, structural modeling tools, and hybridoma/cell culture databases can be found be... | biostars | {"uid": 45666, "view_count": 3733, "vote_count": 1} |
Hi,
I have few quick question regarding macs14?
- How one can treat the replicates? Do I have to run separately and then take average from the final peaks or is there any way to include it in one run?
- macs14 generates two wig files under "--single-profile" option; one for control and one for treated. whi... | If you have the replicate, you can take the consistent peaks called in both replicates. There will be variability in ChIP-Seq data, so sometimes you may want to consider union of peaks instead of intersections.
Regarding peak profile, by control do you mean input ? or control in the sense of WT/KO ? You can plot bot... | biostars | {"uid": 380429, "view_count": 1201, "vote_count": 3} |
hi, I would like to create a list of random mm10 genomic coordinates with bedtools. I saw that the useful command to do this is `bedtools random [OPTIONS] -g <GENOME>`. The problem is that they must have different length, similar to my coordinates:
> summary (new $ width)
Min. 1st Qu. Median Mean ... | There are a couple of different ways to approach this, I think, depending on what you have on hand. If you already have a set of coordinates such as the ones you've entered above, you could simply shuffle these coordinates along the genome using bedtools [shuffle][1]. If you only have a small list of such regions and n... | biostars | {"uid": 9540657, "view_count": 305, "vote_count": 1} |
<p>So I have a 6 lists of differentially expressed genes taken at different periods of time. I need a way to show overlap in the genes that recur between lists. Naturally I tried to make a venn diagram, but 5-6 list venn diagrams are hard to follow. Is anyone aware of other methods of presenting data like this? I'v... | <p>UpSetR is a recently released R package with powerful graphics for visualizing intersections in complicated cases such as yours.</p>
<p>https://cran.r-project.org/web/packages/UpSetR/index.html</p>
| biostars | {"uid": 152450, "view_count": 2241, "vote_count": 2} |
Hi all,
I have an RNA-seq dataset (comparing two different conditions) that I have analyzed using four different methods of differential expression (DE) analysis: DESeq2, limma-voom, liimma-trend, and edgeR. From these 4 different DE analysis, I get the set of raw p values (uncorrected for multiple hypothesis test) fo... | My two cents / thoughts:
A DE program is supposed to give you a list of DE genes, testing the null hypothesis that gene is not DE. You have your list of DE genes that way. Just pick a DE program and stick with it.
There are a few problems with your approach:
1) Such an approach has not been benchmarked (most DE prog... | biostars | {"uid": 9556573, "view_count": 291, "vote_count": 2} |
I have a pipeline which looks something like below, its written in bash
Trimmomatic --> Samtools --> Smalt --> Lastz --> custom perl programs.
If anyone of those processes fails they usually return a non-0 exit code, usually a `1`.
However, my pipeline program will continue to run, report the error and return an... | You're looking for `set -eo pipefail`. Add that after the first (`#!/bin/bash`) line and your script will fail if any part of your script fails.
See for more information: https://vaneyckt.io/posts/safer_bash_scripts_with_set_euxo_pipefail/ | biostars | {"uid": 300840, "view_count": 9609, "vote_count": 1} |
<p><br />
I have plant genomic reads (WGS method) through hiseq 2000 with paired-end reads (read1.fastq, read2.fastq). I need to remove chloroplast and mitchondria reads to assemble only nuclear reads. I need to know which is best and fast way to remove contaminants</p>
<p>1. First doing genome assembly and remove ... | <p>Option 2 is better, mapping with BWA is fast, and you are reducing the total reads to assembly, therefore your assembly time and complexity is reduced.</p>
| biostars | {"uid": 101913, "view_count": 6726, "vote_count": 2} |
A colleague of mine and I have just been discussing the meaning of fold changes and though this question has been asked before non of the answers are actually as straight forward as needed so lets try here to solve this once and for all.
I list here what I understand so far and will update it from your answers.
W... | Percent change = 2^(fold change) * 100, where the baseline then correspond to 100%
log2FC = 2 : 2^2 * 100 = 400, where the baseline then correspond to 100%
Log2FC = -2 : 2^-2 * 100 = 25, where the baseline then correspond to 100%
Hope this helps | biostars | {"uid": 342756, "view_count": 62393, "vote_count": 15} |
I have list of genes like
LOC109802912
LOC109788332
LOC109789928
LOC109809764
...
and have a fasta file like
>rna-XR_003803819.1 gene=LOC114915746
TGCTTCTTCTCTGTTGGAAGAGTTTAAAAGCAATAAAACTAAGTGTTTTGAGCTCTCTGAAATTGCTGGT
CATGTTGTTGAGTTCAGTGCGGATCAATATGGGAGCCGATTTATTCAGCAAAAGCTTGAAACAGCTAc... | Try this:
pip install --user pyfaidx
xargs faidx -d " " YOURFASTA.fasta < GENEID_LIST.txt > extracted_sequences.fasta
| biostars | {"uid": 439929, "view_count": 554, "vote_count": 1} |
Hi all,
I am using R script from Getting Genetics Done ( http://www.gettinggeneticsdone.com/2014/05/r-volcano-plots-to-visualize-rnaseq-microarray.html) to generating Volcano plots but my problem is how to show particular single gene name on volcano plot without any condition (i.e foldchange or pvalue). I just wan... | Perhaps I missed something, but it looks quite obvious to me:
with(subset(res, Gene == "WNT7A"), textxy(log2FoldChange, -log10(pvalue), labs=Gene, cex=.8))
| biostars | {"uid": 262817, "view_count": 5102, "vote_count": 2} |
<p>I have a very fundamental question that I can't seem to find an answer to.</p>
<p>I have a variety of TF and histone marks for a untreated cell line and a treated cell line. I ran a tool that returned a bed file of 'potential' enhancer regions. The untreated cell line identified 36k possible enhancer ... | I would do check how many enhancer sites are common b/w two conditions
- If high overlap (>90%), I would conclude, treatment has no significant effect and would proceed by the plotting the enrichment of histone marks/TF on the intersection or union (if >95% overlap) of enhancer regions
- If low overlap or very di... | biostars | {"uid": 175258, "view_count": 1745, "vote_count": 2} |
GenCode has a wonderful breakdown of the number of coding/non-coding genes and transcripts here...
http://www.gencodegenes.org/stats.html
Does a similar breakdown exist for RefSeq anywhere? Thanks! | I don't believe RefSeq do as good a breakdown of transcript types as GENCODE, however, you may be interested in the following resources:
- <a
href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S8-S2">Comparison
of GENCODE and RefSeq gene annotation and the impact of reference
gene... | biostars | {"uid": 300143, "view_count": 1534, "vote_count": 1} |
Hello,
I am trying to figure out how DESeq2 calculates its log2FC measure - we see a strange pattern in the FCs in our data and I'd like to reproduce them by hand from scratch to make sure this pattern does not reflect an error with my pipeline.
Right now, I'm doing this:
deseqOutput<-DESeq(data_collapsedT... | Take a look at [this thread][1] and the [DESeq2 manuscript][2]
They are using a moderated (shrinkage) estimate.
[1]: http://seqanswers.com/forums/showthread.php?t=49101
[2]: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8 | biostars | {"uid": 178010, "view_count": 3435, "vote_count": 1} |
I'm building a Snakefile and getting an error I'm struggling to fix when trying to add the `log` parameter in my homer annotation rule.
Here is the Snakefile:
threshold="25 33 5 66 75".split()
rule all:
input:
expand("homer_files/annotation_files/ATAC24to31_fetal_hMG_consensusPeak.{T... | It was a typo in the braces!
log:
"logs/homer/annotation.ATAC24to31_fetal_hMG.consensusPeak.(THRESH}.log" | biostars | {"uid": 380849, "view_count": 2466, "vote_count": 1} |
Hello,
I am trying to use a for loop in python to loop through a bam file and take out reads that map to certain chromosomes, for further downstream analysis. I am having problems in the beginning, seemingly easiest part of my code.
samfile = pysam.Samfile("mybam.bam", "rb")
positions=["7:15197085... | Answered my own question [from StackOverflow][1]
[1]: http://stackoverflow.com/questions/10255273/iterating-on-a-file-using-python | biostars | {"uid": 178405, "view_count": 4136, "vote_count": 1} |
Deeptools is an incredible package, but I want more plotting versatility.
Anyone kind enough to share workflow/code for plotting computeMatrix heatmaps and average plots in R (ggplot, pheatmap etc.)?
Other suggestions for plotting from .bw coverage files and .bed feature files?
Thanks a lot!!! | I'm not sure it'd make sense to tidy a matrix of that size for use with ggplot2. Below is how to read a simple file produced by computeMatrix in R (the example file I'm using below can be found in the deepTools source code under `deeptools/test/test_data/`):
m = read.delim("computeMatrixOperations.mat.gz", skip=... | biostars | {"uid": 319187, "view_count": 6938, "vote_count": 2} |
I got the good quality genome IDs for 54000 genomes like below:
#genome
G001281285
G000014725
G000775715
G000254175
G001380675
G900057405
G001076295
and I also got all 74000 genome sequence files compressed in fna folder like below
cd fna/
G001284865.fna... | for i in $(cat list.txt); do mv "$i".fna.bz2 fna/filtered/; done
Where list.txt is your list of high quality genomes and filtered/ is a new directory. | biostars | {"uid": 454937, "view_count": 1295, "vote_count": 1} |
Hi,
I am using RMarkdown in Rstudio and I want to execute commands from a program using a bash chunk
````{bash}
```
I have a program called samtools on my computer so when I execute it in the chunk, it works.
```{bash}
samtools
```
When I type :
```{bash}
which sa... | You can use the full path to the tool:
```{bash}
~/bin/bioinfotools/vcftools
```
Returns:
##
## VCFtools (0.1.16)
## © Adam Auton and Anthony Marcketta 2009
##
## Process Variant Call Format files
##
## For a list of options, please go to:
## https://vcf... | biostars | {"uid": 400685, "view_count": 7174, "vote_count": 2} |
I am very new to RNA-Seq. I am trying to align my samples with STAR. I am generating the genome index myself. Because I was hoping to add the spike-in sequence to the GTF and FASTA files.
I am downloading the GTF file from here: ftp://ftp.ensembl.org/pub/release-86/gtf/mus_musculus/
There are 2 GTF files one wit... | The one without 'chr' contains annotations for genes on unplaced or unlocalized contigs, while the one with 'chr' only contains annotation for assembled chromosomes, both of them have no prefix 'chr' in chromosome name, see this example:
zcat Danio_rerio.GRCz10.87.gtf.gz | cut -f1 | awk '{dict[$1]++}END{for(i in... | biostars | {"uid": 217700, "view_count": 11902, "vote_count": 7} |
Hi,
I would like to filter out some sequences from a fasta file by using a specific pattern.
For example I have this file:
```
>input1
UGAGGUAGUAGG
>input2
CUAUGCUUACC
>out1
UCCCUGAGACCGUGA
>out2
CUCCGGGUACC
>desc1
ACUUCCUUACAUGCCC
```
I know already how I can extract all the fasta sequences with a specific pattern... | I like Pierre's answer to this since it's simple. However, I had been thinking about adding regular expression filtering to my [pyfaidx][1] project, and this morning I finished up adding this functionality:
```
$ pip install pyfaidx
$ faidx in.fasta -g "out" > out.fasta
```
The (small) advantage here is that faidx wi... | biostars | {"uid": 133245, "view_count": 7571, "vote_count": 2} |
I don't understand in samtools tview the signification of an underlined read.
I understand what orphan means (in paired end, the other pair end is not mapped), but what secondary means? it means it's a duplicate ? Sometimes I can have two reads with the same name underlined and I don't know how to analyze them.
I fou... | <p><strong>Secondary</strong>: the read was mapped elsewhere (primary location). This position is another candidate position for this read.</p>
| biostars | {"uid": 140999, "view_count": 4045, "vote_count": 1} |
Hi ,
I would like to plot a bed file with numeric values ( = bedgraph).
My input data are : chr pos start end value ( value between -1 and 1)
exemple :
chr19 50906809 50907015 0.8173737057494912
chr19 50909381 50909562 0.2639404477044525
chr19 50909499 ... | I just discovered the Sushi package which do the job pretty well !
https://bioconductor.org/packages/release/bioc/html/Sushi.html
See [plotbedgraph][1]
[1]: https://www.rdocumentation.org/packages/Sushi/versions/1.10.0/topics/plotBedgraph | biostars | {"uid": 306085, "view_count": 6589, "vote_count": 2} |
<p>Hey everyone,</p>
<p>I am trying to transpose large datasets in excel but it keeps giving me the message we can't paste because copy area and paste area aren't the same size. Is there a way to transpose all the data at one time instead of piece by piece? One dataset has a great amount of rows and columns.... | Stack Overflow <a href="http://stackoverflow.com/a/1729980/19410">offers a solution</a> that uses GNU *awk* and should run considerably faster than R (if you plan on doing a lot of transposing).
Also something to keep in mind is that Excel makes Microsoft-y text files. You may need a tool like <a href="http://source... | biostars | {"uid": 150611, "view_count": 17946, "vote_count": 2} |
Hi there,
Could anyone explain me a little bit these two lines of my GVCF file?
Why I'm getting "NON REF" alternative allele? And why for the second line I only see END information and not the rest?
```
GL000192.1 546636 . G A,<NON_REF> 49.77 . BaseQRankSum=1.026;ClippingRankSum=1.026;DP=4;MLEAC... | <p>OK, I found the solution in GATK manual (<a href="https://www.broadinstitute.org/gatk/guide/article?id=4017">https://www.broadinstitute.org/gatk/guide/article?id=4017</a>). I'll answer my own question just in case that someone else have the same issue.</p>
<p><em>"The first thing you'll notice, hopef... | biostars | {"uid": 128817, "view_count": 7765, "vote_count": 7} |
Hi.
I'm trying to annotate gene symbols next to probe IDs (Affymetrix Mouse Gene 1.0-ST Array).
I used "mogene10sttranscriptcluster.db" package (v8.7.0) of R for the annotation.
But here's the problem.
1) Using mogene10sttranscriptcluster.db directly
library(mogene10sttranscriptcluster.db)
... | I found my own answer.
It seems like the mogene10sttranscriptcluster.db utilizes org.Hs.eg.db for annotation.
And the version of org.Hs.eg.db is different between mogene10sttranscriptcluster.db and AnnotationDbi.
I found this because when I loaded different version of org.Hs.eg.db, the same version of mogene10... | biostars | {"uid": 380939, "view_count": 1154, "vote_count": 1} |
I have a list of genes from an Affymetrix microarray analysis.
However I have duplicate genes, I wonder how do I collapsed to unique genes by calculating the mean expression of transcripts from the same gene locus?
Any information is valid.
Thank you! | Hello Joe,
You can use `aggregate()` or *limma*'s `avereps()` function.
Kind regards,
Kevin | biostars | {"uid": 407358, "view_count": 2072, "vote_count": 1} |
Hi,
Do you know what these letters like R, Y, S, G... (in genotype column) mean in output file from VarScan? Or do I always need to generate a VCF file if I want to know the genotype in that position for tumour and normal samples?
<a href="https://ibb.co/qp6YQD5"><img src="https://i.ibb.co/SBSwC6r/gt.png" alt="... | [degenerate notation][1] ?
[1]: https://en.wikipedia.org/wiki/Nucleic_acid_notation#IUPAC_notation | biostars | {"uid": 484409, "view_count": 523, "vote_count": 1} |
Dear Biostars,
I'm a new PhD student and my main project is the identification/Differential Expression of piRNAs in Human colorectal cancer (CRC) cell lines with smallRNA-seq.
I would like to ask about the bioinformatic analysis workflow and which databases/libraries for different small RNAs
I have found various str... | Welcome to the wonderfully strange world of piRNAs :) I will first urge to read two of my previous answers on the subject:
https://www.biostars.org/p/235278/#235289
https://www.biostars.org/p/179944/#228109
TLDR; if you are novice, use piPipes. Very easy to set-up, specially if you are working with human data, a... | biostars | {"uid": 347827, "view_count": 2902, "vote_count": 4} |
Hello!
I am attempting to remove host cell line reads from viral reads for a viral genome sequencing effort. (Miseq 2x300 Nextera). I downloaded and set up deconseq according to the install file, and generated a database using bwa64 on my desired genome. This worked great and I was able to filter the host genomic read... | bwtsw is only for large genomes..see
https://www.biostars.org/p/53546/ | biostars | {"uid": 143866, "view_count": 3078, "vote_count": 1} |
I have analyzed RNA-seq data with DESeq2 and am trying to plot a 3D PCA using rgl-plot3d.
I was trying to output PC1, PC2, and PC3 and then plot them. However, I realized that I get different results for PC1 (and PC2) when I try plotPCA (used with DESeq2) and prcomp.
What is the bug on my code?
dds <- DESe... | `plotPCA` by default uses the top 500 most variable genes prior to `prcomp`, and you used all genes.
Check the source code of `plotPCA` for details, e.g. by typing `getMethod("plotPCA","DESeqTransform")` in `R`.
Edit: Cool, https://www.biostars.org/u/41557/ and https://www.biostars.org/u/1767/ gave the same answers... | biostars | {"uid": 416573, "view_count": 3896, "vote_count": 2} |
<p>I should start by saying I have solved this problem, but I feel like my code is ugly and overkill.</p>
<p>I am trying to sort a dataframe on a column containing human chromosomes:</p>
<p>chr1,chr2...chrY, chrX.</p>
<p>the problem is:</p>
<p>chr1, is followed by chr10. </p>
<p>What tricks do you use to deal wit... | <p>the mixedsort is pretty good, but it will think ChrM comes before ChrX, then ChrY</p>
<p>if you have your own arbitrary order you should just use factors</p>
<pre><code>> df<-data.frame("chr"=c("chr1","chrM","chr10","chr2","chrX","chr2"),"val"=c(1,2,3,4,5,6))
> df
chr val
1 chr1 1
2 chrM 2
3 chr10... | biostars | {"uid": 17224, "view_count": 9162, "vote_count": 6} |
<p>I have this genome of a transposase from ciliate protozoa, i need to identify if the genome is from macronucleus or from micro nucleus, for that i have to know if it is from linear DNA or from circular DNA, how can i design an experiment for this genome sequence to know which nucleus it is from?</p>
| <p>I only have this Genome sequences, from Ciliate cell, only the sequence is known,</p>
| biostars | {"uid": 102378, "view_count": 1869, "vote_count": 1} |
I was trying to use this fgsea library for enrichment analysis but there was this error coming up due to some issue with BiocParallel , it was resolved by adding this line `register(SerialParam())` to the code .
Original [source][1] with a bit of modification
Error in registered()[[bpparamClass]] :
... | I experienced the same thing just now on a not so well patched computer running an older version (R3.4.4/fgsea_1.0.2/BiocParallel_1.8.2) but tried it on another computer that I keep better updated (R3.5.2/fgsea_1.8.0/BiocParallel_1.8.2) and it worked. My advice would be to upgrade your R installation to the latest one ... | biostars | {"uid": 327699, "view_count": 3941, "vote_count": 1} |
Hello all, I've recently started with DNA-related analysis, and was wondering, whether, if I take:
https://www.ensembl.org/info/data/ftp/index.html (cDNA)
does this represent, for example, the human exome? If not, what are the differences, and how can one obtain the missing information then?
Thank you! | the cDNA file will contain all mRNAs of the human genome. It will be CDS + UTR (if available) and thus represents the transcribed part of the genome that will eventually be translated into proteins. | biostars | {"uid": 339805, "view_count": 1187, "vote_count": 1} |
If I want to read a bam like this
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <htslib/sam.h>
int main(int argc, char *argv[]){
samFile *fp_in = hts_open(argv[1],"r"); //open bam file
bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //read header
... | I think you could call the following for each read:
bool is_reverse = bam_is_rev(aln);
See: https://github.com/samtools/htslib/blob/6e86e386bed5c80c5222bd2e8eb2fd8c99234909/htslib/sam.h#L200-L205
It's a convenience macro for the call described in Pierre's answer. You might need to add:
#include <std... | biostars | {"uid": 344069, "view_count": 1767, "vote_count": 1} |
I have just over 100 files from an RNA-seq experiment and I have working on converting these BAM files to Bigwig files for visualization on UCSC Genome Browser.
I am new to the field of RNA-seq but from what I understand, I need to scale/normalise the BAM files before conversion to bigwig format. There appear to be ... | The most convenient solution is IMHO `deeptools bamCoverage`. It offers multiple options for normalization, binning and strand-specificity. Have a look at the [docs][1].
[1]: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html | biostars | {"uid": 333137, "view_count": 2373, "vote_count": 2} |
Hello biostars,
I have a FASTA file of about 300 kbp & I have several sequences (400 bp - 800 bp) that I want to search in there.
I tried using BLAST, but I couldn't find the option to allow me to upload my own FASTA file in the Search Set box.
I tried this:
http://www.ebi.ac.uk/Tools/psa/emboss_water/nucleot... | You can use the command line version of blast+ to create a database out of your sequences (using `makeblastdb`) and then blast your query sequence against this database. It is not possible to do what you want on the web. | biostars | {"uid": 250341, "view_count": 2725, "vote_count": 2} |
Hi,
I would like to compare cytokine levels of four groups of mice with different treatments. There are four to six mice in each treatment group, so the sample size is not large. The standard deviation of most cytokine levels in each treatment group are much larger than their mean.
Also, there are many zero in d... | Mann-whiteny test can be used as a non-parametric test to compare the median of two independent groups (samples do not follow normal distribution) | biostars | {"uid": 191264, "view_count": 1693, "vote_count": 1} |
Hello all,
I have a list of GO terms and I would like to create the corresponding network. Even better, I would like to be able to create the *entire* GO metabolic network and then highlight my terms in that network.
I have two challenges: I am studying Microbiome, which is largely unknown/predicted genes, so I ... | This is how I accomplished the task of making the GO network in Cytoscape.
1) Download go.obo from http://geneontology.org/page/download-ontology
2) Run my python script to convert go.obo to GO.cytoscape.sif file
3) Cytoscape -> Import -> Network -> File, select the GO.cytoscape.sif file
PRESTO, the full networ... | biostars | {"uid": 193587, "view_count": 6546, "vote_count": 2} |
Hi guys,
I need to identify insertions of specific sequences in my genomes. I have WGS data with read length of 250 nucl. Previously I was working on identification of large sequences insertions and simply looked for discordantly mapped reads for that using bowtie2 and bbmap.
Now I am looking for sequences that ar... | You can call insertions near read length with BBMap like this (assuming paired interleaved reads that mostly overlap):
bbmerge.sh in=reads.fq out=merged.fq
reformat.sh in=merged.fq out=filtered.fq minlen=350
bbmap.sh in=filtered.fq out=mapped.sam ref=ref.fa slow
callvariants.sh in=mapped.sam out=v... | biostars | {"uid": 259835, "view_count": 2263, "vote_count": 1} |
Does anyone know what the difference is between the Coriell sample NA12878 and the NIST sample RM 8398? As far as I can tell, RM 8398 and NA12878 are extracted from the exact same cell lines, except the Coriell sample is $84 and the NIST sample is $453. Links are below:
NA12878: https://www.coriell.org/0/Sections/Se... | The NIST source preparation material discusses how RM8398 was extracted from the NA12878 cell. It notes that the cell lines are subject to mutation and so the sequence can start to vary over time. NIST controls for this by producing a large batch of NA12878 and mixing the extracted DNA to reduce the variation between t... | biostars | {"uid": 339082, "view_count": 2718, "vote_count": 1} |
Hi all,
I am looking for a test data set for some software I'm developing, which would be small and simple, but still biologically meaningful. What I need is raw Illumina-style NGS data - basically Fastq format files (paired end). I thought that a phage genome might be a good choice due to it's small size and simpli... | http://www.ncbi.nlm.nih.gov/sra/?term=phage | biostars | {"uid": 209903, "view_count": 6130, "vote_count": 1} |
I wonder what is the relationship between Plink *.tped* and *.ped* files. From what I observe, it seems it is more complicated than a simple transpose.
For example, in Section 4.1.1 of [this manual][1], there is an example as following:
```
1 1 0 0 1 1 1 1 G G
1 2 0 0 ... | Interesting, I didn't know about that! Could it be that PLINK internally just sorts the alleles using some arbitrary rules?
I just ran a test with input alleles "G A", "A G" in various combinations with other SNPs and they always came out as "G A" in the transposed dataset.
Similarly, "G T", "T G" always becomes ... | biostars | {"uid": 168804, "view_count": 3675, "vote_count": 3} |
Suppose I have a list of genes obtained from an experiment using mice. Now I have to perform an enrichment and I can choose to perform it using mouse GO terms, human GO terms, etc...
Is it ok to use human GO terms over mice genes?
If yes, then why bother creating specific mouse GO terms? I understand that mice ma... | Gene sets such as GO terms are developed by integrating the current scientific knowledge about the function of genes. Even in the case when you use human GO terms in human, many of the functions of those human genes which are "summarized" by the human ontologies, have actually been (at least in part) first discovered i... | biostars | {"uid": 472892, "view_count": 787, "vote_count": 1} |
Hello,
I wanted to inspect the (non-N) regions that were added in, in GRCh38/hg38 that were not there in GRCh37/hg19. Is there a hg38 bed file with those "new" regions somewhere or is there an easy way to get that without lifting over again?
Thanks for your help! | I used the excellent remap service from NCBI:
http://www.ncbi.nlm.nih.gov/genome/tools/remap
to go from my hg19 assembly to my hg38 assembly.
I made a dummy bed file using the chromosome lengths, which you can get from here:
`mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from ... | biostars | {"uid": 195827, "view_count": 1888, "vote_count": 1} |
For a single paired end read the script is
hisat2 -x /path/to/hg19/indices -1 sample_1.fq.gz -2 sample_2.fq.gz | samtools view -Sbo sample.bam -
Our queue is full so I'm not able to test this but is it possible to allign multiple paired end reads in one go and how would I go about it?
| Probably your `sample_1.fq.gz` and `sample_2.fq.gz` **files** already contain multiple **reads** inside. I guess you want to align multiple files, right?
But do you want the output in a single file, or multiple files as output? For the former, you can pass a comma-separated list of files to hisat2 (see `-1` and `-2... | biostars | {"uid": 293107, "view_count": 4763, "vote_count": 1} |
Hello
I need to convert gene stable ID like this (ENSMUSG00000028461.12) to gene name. I used Biomart and I have a list of gene stable ID. I don't know how to join mine list with Biomart together, because Biomart gene stable ID list has not the decimal number in ID, do you have any idea?
thanks | Hello,
I don't understand whether your problem is that your input has version numbers or that the output of biomart hasn't. Nevertheless we can solve both:
For the input choose under `Filters` the category `Input external references ID list` and select in the drop down `Gene stable ID(s) with version`.
For the... | biostars | {"uid": 332886, "view_count": 3155, "vote_count": 1} |
I have a large fasta file of 16S sequences and I want to retrieve sequences using a list of organism names. Do you know a script capable of doing it?
EDIT:
Headers look like that:
```
>S000000859 Bacillus sp. USC14; AF346495
sequence
>S000001027 Paenibacillus borealis; KN25; AJ011325
sequence
```
And I have a list ... | As your list is containing 'Paenibaci' in common, I have followed this approach
```
grep '^>' input.fasta > headers.txt
sed -n '/Paenibaci/p' headers.txt > filter_headers.txt
$ ./faSomeRecords input.faa filter_headers.txt output.faa
```
https://www.biostars.org/p/136926/#136928 | biostars | {"uid": 141241, "view_count": 14949, "vote_count": 3} |
Dear all,
I am working on circular RNA and miRNA. I used the tool DCC to get possible circular RNA candidates from my STAR alignment. Since it is know that circular RNA expression can effect miRNA in various ways (et vice versa), I would like to compute the likelihood that one specific circRNA binds to a miRNA (or vic... | Hi!
I have work a little on circRNA too, and as far as I know, there is no resource for doing what you want. However, in order to resolve your question, there are some web servers that could be helpful to address your problem:
> I would like to compute the likelihood that one specific circRNA binds to a miRNA (... | biostars | {"uid": 258242, "view_count": 2541, "vote_count": 2} |
Hi all,
I have fastQ file and I need to rename it using `sed` command. below the explanation :
The read names in my files are
```
@HWI-ST365:251:D0RP0ACXX:5:1101:4471:2213#12_1
@HWI-ST365:251:D0RP0ACXX:5:1101:4471:2213#12_2
```
And i want to transform them in the format:
```
@HWI-ST365:251:D0RP0ACXX:5:... | Well, you're very close to the solution. You only need to scape to '`/`' character: `sed -i 's/_/\//g'` should work.
Just a little advice, try to call to sed command in the following way:
cat file.fq | sed 's/_/\//g' > reformat.fq
In this way you can go back to the original input file in the case that some... | biostars | {"uid": 185065, "view_count": 5212, "vote_count": 2} |
Hi All,
I would like to ask that is there an accurate tool/script for deinterleaving fastq files? I managed a 'bam to fastq' conversion according to http://gatkforums.broadinstitute.org/discussion/2908/howto-revert-a-bam-file-to-fastq-format and I would like to deinterleave the output fastq.
Many thanks! | [Reformat][1] can do that, if you're sure the resulting fastq file is interleaved. You can run with the "vint" and "ain" flags to verify that it is interleaved properly. If it's not, you can fix it by running repair.sh (also in the BBMap package).
[1]: http://seqanswers.com/forums/showthread.php?t=46174 | biostars | {"uid": 141256, "view_count": 9567, "vote_count": 2} |
Hello guys,
Is there any database where I can download transcription factor's sequences, like if I want to download all the known transcription factors sequences of Tribolium castaneum (let's say), how can I do that?
i wanna compare them with a transcriptome in a fasta file. | <p>For the beetle you mentioned it doesn't look like there's a dedicated resource, in general this isn't exactly trivial. You could use BioPython/Java/etc or entreztools and download by searching for specific terms, however the success of this depends on the completion and quality of the annotations availab... | biostars | {"uid": 123431, "view_count": 1936, "vote_count": 1} |
End of preview. Expand in Data Studio
Dataset Summary
This dataset contains 4803 question/answer pairs extracted from the BioStars website. The site focuses on bioinformatics, computational genomics, and biological data analysis.
Dataset Structure
Data Fields
The data contains INSTRUCTION, RESPONSE, SOURCE, and METADATA fields. The format is described for LAION-AI/Open-Assistant
Dataset Creation
Curation Rationale
Questions were included if they were an accepted answer and the question had at least 1 vote.
Source Data
Data collected using the Biostars API
Additional Information
Dataset Curators
@cannin. @cannin has no affiliation with the BioStars project.
Licensing Information
Apache-2.0
Citation Information
BioStars Project
Cite the original project: https://doi.org/10.1371/journal.pcbi.1002216
This Dataset
Citation for this dataset:
@misc{Luna2023a,
author = {Augustin Luna},
title = {biostars_qa Dataset},
year = {2023},
howpublished = {\url{https://huggingface.co/datasets/cannin/biostars_qa}}
}
This Dataset Code
Citation for the code to generate this dataset:
@misc{Luna2023b,
author = {Augustin Luna},
title = {biostars_qa Code},
year = {2023},
howpublished = {\url{https://github.com/cannin/biostars_qa}}
}
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