INSTRUCTION stringlengths 48 14.1k | RESPONSE stringlengths 14 8.79k | SOURCE stringclasses 1
value | METADATA stringlengths 48 55 |
|---|---|---|---|
Hi all,
I have been trying to use Mutect to compare results from Varscan and other tools. To run MuTect, pre-processing from GATK and Picard tools is necessary.
1\. **Mapped reads using BWA.**
2\. **Convert to sorted BAM using PICARD**
```
java -Xmx4g \
-Djava.io.tmpdir=/tmp \
-jar SortSam.jar \
SO=coordinate... | you have to specify the read group from the beginning using the option -R of bwa
> `-R STR` Complete read group header line. '\t' can be used in STR and will be converted to a TAB in the output SAM. The read group ID will be attached to every read in the output. An example is '@RG\tID:foo\tSM:bar'. [null]
you can add... | biostars | {"uid": 115819, "view_count": 24229, "vote_count": 6} |
<p>Hi,</p>
<p>I have a bam files produced from mapping by LifeScope Tool (mapping of SOLiD reads). I would like to know the length of the reads that were mapped to the reference genome based on the information present in bam files. Is there a tool which can give me the stats of such things from bam files?</p>
<p>Than... | A little shorter version:
samtools view test.bam | awk '{print length($10)}' | head -1000 | sort -u
| biostars | {"uid": 65216, "view_count": 48209, "vote_count": 7} |
Hello,
I've been given some data to perform differential expression on, and it the process of QCing the resultant count data, I'm seeing that the library sizes have pretty big discrepancies between the 2 samples shown below. I know a good run of an illumina generates between 10-40 million reads, but is it normal for... | Differences in depth are not *per se* a problem. It is only a problem when depth is so low that many genes have zeros (dropouts) due to the under-sequencing. Zeros will remain zeros, regardless of the normalization method. Usually you run PCA first to see whether this sample manifests as an outlier. If so you can eithe... | biostars | {"uid": 9551775, "view_count": 556, "vote_count": 1} |
Hi, I used "macs2" to call peaks from my data of ChIP-seq.
This is not my first time to use macs2, but still found myself not being able to grasp what "gappedPeak" stands for in the OUTPUT of macs2.
"NAME_peaks.narrowPeak" , "NAME_peaks.broadPeak" are quite intuitive,
"narrowPeak" means narrow peaks which is s... | GappedPeak is a representation of narrow peaks as blocks over a broad peak. To trick the visualisation tools, they use the same format as gene models, but use the narrow peak coordinates as exons coordinates and the broad peak coordinates as coding region coordinate. | biostars | {"uid": 242501, "view_count": 4969, "vote_count": 2} |
Dear All,
I have a VCF file and I want to change part of the header:
```
##contig=<ID=1,length=195471971>
##contig=<ID=10,length=130694993>
##contig=<ID=11,length=122082543>
##contig=<ID=12,length=120129022>
##contig=<ID=13,length=120421639>
##contig=<ID=14,length=124902244>
##contig=<ID=15,length=104043685>
##contig... | I have **not tested/validated** the commands, but think you need two steps: 1) change the header(s)
bcftools view --header-only $INPUT_FILE | sed 's/##contig=<ID=/##contig=<ID=chr/' | sed 's/##contig=<ID=chrMT/##contig=<ID=chrM/' > $OUTPUT_FILE
and 2) change the data field (as questioned by [@charlesberkn][1]).
... | biostars | {"uid": 160863, "view_count": 9280, "vote_count": 2} |
Hi all,
Is there a tool to calculate the combined length of transcripts which map to a given interval. For example as a function of bedtools or htseq? I can calculate the number of reads mapping to a particular gene using these tools but not the length of the gene segment which has been covered. What I want to know is... | BEDOPS <a href="http://bedops.readthedocs.org/en/latest/content/reference/statistics/bedmap.html#element-and-overlap-statistics">*bedmap --bases* and *bedmap --bases-uniq*</a> offer total and distinct counts of bases of map elements (*e.g.*, transcripts or reads) which overlap ("map" to) a reference interval (*e.g.*, a... | biostars | {"uid": 166585, "view_count": 1798, "vote_count": 2} |
<p>I have paired-end RNA-Seq data - read1 and read2 - stored in the same fastq file.</p>
<p>I'd like to align the reads using tophat.</p>
<p>Do I have to separate the data into two different files before running tophat?</p>
| If you have any pattern in the read name ( like `1:N:####` or `/1` or `_1` etc) you could use the <a href="http://homes.cs.washington.edu/~dcjones/fastq-tools/fastq-grep.html">fastq-grep</a> to match the pattern to extract the R1 and R2 into two separate files.
Or a simple Awk patter match will do. something like:
... | biostars | {"uid": 123686, "view_count": 5479, "vote_count": 2} |
Hello,
Our lab would like to use [Homer][1] and install it under the following environment:
- Mac OS X 10.8.5
- Xcode Version 5.0.1 (5A2053)
- Xcode command line tools
- Homebrew
- Python 2.7.2 @ /usr/bin/python
It looks like Homer was successfully installed except for one package, seqlogo. The results of our troubl... | <p>Follow the weblogo install directions found <a href="http://homer.salk.edu/homer/introduction/install.html#Installing_3rd_Party_Software">here</a> you will need a specific version that might not be the right one installed by pip</p>
| biostars | {"uid": 113042, "view_count": 8556, "vote_count": 3} |
Hi,
I've downloaded a set of bams from Illumina's Platinum Genomes experiment (hosted at EBI) and would like to do due diligence and perform a checksum check, but I can't find any published for these files.
Has anyone else downloaded the bam files from ftp://ftp.sra.ebi.ac.uk/vol1/ERA172/ERA172924/bam/ and run `md5su... | EBI are actually very good at storing their data and usually have the md5 checksums among the files.
To find the md5 number for your data: look at their data table for the accession number instead of raw FTP access: https://www.ebi.ac.uk/ena/data/view/ERA172924&display=html
Click on "select columns", then on "submitt... | biostars | {"uid": 137254, "view_count": 2952, "vote_count": 1} |
Hi
I've done PCA for my gene expression data after DEG analysis, I can see that my case and control samples clustered distinctly but **I want to report a p.value for this result**, it worth to notice that I have the coordinate csv file that represents coordinates of samples from different phenotypes (case vs control)... | PCA is an exploratory data analysis method. It does not test a null hypothesis and generate a p-value.
If you want to compute a p-value maybe you should try pvclust package in R. It didn't use PCA but a hierarchical clustering and report p-values for each sub-tree
http://stat.sys.i.kyoto-u.ac.jp/prog/pvclust/ | biostars | {"uid": 279919, "view_count": 10560, "vote_count": 1} |
<p>I got RNASeq data in several samples. I checked the FastQC, seems the read quality are good (Hiseq 2000). But the problem is many reads are mapped to intronic region, and the regions have no any reference exons there (Refseq, ensembl, gencode). We don't know what they are. We guess the problem happend in library pre... | <p>If you have a bed file of exonic regions, or gtf, something like that, you can use <a href='https://code.google.com/p/bedtools/'>BEDTools</a> to filter your .bam for reads that fall in the desired coordinates, using intersectBed</p>
| biostars | {"uid": 73821, "view_count": 3976, "vote_count": 1} |
Hello,
Actually I am doing a tutorial (https://hakyimlab.github.io/psychencode/generate_weights.html) where they indicate that I need a dbSNP150 reference table containing "chromosome, position, ref, alt, rsid, and dbSNPBuildID" information for the hg19 version of the human genome. I am stuck in this step, can anyone ... | Since you are working in R, you can often use annotation that is provided as part of Bioconductor. The latest release of Bioconductor for example contains a copy of dbSNP [version 150][1] and [even newer ones][2].
However, the annotation provided by Bioconductor refers to another reference genome build (hg38 instead ... | biostars | {"uid": 9526352, "view_count": 613, "vote_count": 1} |
I'm reading [this excellent paper][1] which describes a methodology to standardize variant benchmarking process. They say that the normal binary classification form (i.e., TP, FP, FN, and statistics derived from these) are not simple for variant calls. So they go on to describe how they do this, in tabular form.
It'... | > It's also hard to decipher why the n/a's occur in the rest of the table?
I think it is because those scenarios can't happen. If you compar two individuals, and the Query has var1/var3 then there has to be at least a var2 in your comparison, otherwise you can't have var3.
If Query = GT:1/3 then the only scenari... | biostars | {"uid": 380377, "view_count": 1645, "vote_count": 1} |
Hi all.
I have detected somatic mutation and would like to know its significance for clinical interpretation.
I used MutationMapper in cBioPortal and then got a set of annotated mutations with plot as shown in below.
<img alt="lollipop plot example" src="http://www.cbioportal.org/images/lollipop_example.png" style="... | Your question is an important one without a definitive answer. In terms of clinical annotation, protein domain is just one of MANY, MANY potential features for prioritization. In practice, I would not discard mutations that are not in a known domain. | biostars | {"uid": 139260, "view_count": 3405, "vote_count": 1} |
I've got a list of 237 Ensembl protein IDs (e.g. ENSP00000493027), and I'm trying to convert them to UniProt accession numbers so that I can retrieve their REST text entry (e.g. https://rest.uniprot.org/uniprotkb/A0A286YF28.txt).
Officially, UniProt says to do it [this way][1]:
import urllib.parse
impo... | Here is an example how to access UniProt's REST with Python 3 with the `requests` package (`pip install requests`).
import json
import requests
import time
URL = 'https://rest.uniprot.org/idmapping'
IDS = ['P40925', 'P40926', 'O43175', 'Q9UM73', 'P97793']
params = {
... | biostars | {"uid": 9528992, "view_count": 699, "vote_count": 1} |
My experiment set up: 2 samples from WT mice, 2 samples from KO mice, all sequenced with 10x 3' scRNA-seq. The cell populations sorted for sequencing are the same.
Seurat offers the anchor transfer method to perform dimension reduction and clustering, but differential expression is still performed upon normalized, u... | I personally like to aggregate cells per genotype and cluster into pseudobulks and then simply include the batch information into the design as we do in any normal RNA-seq setup such as `~batch+pseudobulkCluster`. Since you have replicates per genotype this comes then down to a normal 2 vs 2 comparison. That having sai... | biostars | {"uid": 456987, "view_count": 944, "vote_count": 1} |
A student and me are testing the mirDeep2 pipeline on the Drosophila genome. mirDeep2 is using bowtie internally but we got a relatively low mapping rate and therefore also fed the pipeline with an alignment generated by BWA. BWA yielded a larger fraction of aligned reads, and naively I would assume that this should al... | Think we are approaching a first solution to the mirDeep paradox.
## Differences in SAM output ##
Most likely the pipeline is adapted to the peculiarities of the output format of bowtie.
Look at the differences for a random multi-mapping read:
Bowtie:
SRR019717.35 16 2R_dna:chromosome_chromos... | biostars | {"uid": 217254, "view_count": 3909, "vote_count": 4} |
My basic question is why aren't genome assemblers using an underlying [Hamiltonian path algorithm][1]?
My basic, high level understanding of genome assemblers is that they consider nodes in a graph created from short kmer sequences and connect a directed edge when the suffix of one node is the prefix of another. An Eu... | In my view, reducing overlap assembly to the Hamilton Path problem is just an illusion. I could not find the full text of old literatures -- among the papers I know, such a formulation seems to first appear in the 2001 Euler paper, a paper that objects to OLC. Even if there are earlier papers on this formulation, the m... | biostars | {"uid": 157515, "view_count": 4013, "vote_count": 6} |
I have a dataset with a missing column header for first column. How to name it so that I can find it using
a$
![screenshot][1]
[1]: https://image.ibb.co/nNv7Xn/column_name.jpg
<br/>
I used following command but got error
a$miRNAs<-row.names(a)
Warning message:
In a$miRNAs <- row.name... | It is rownames not a column. Since you have mentioned dplyr, we can convert it to columns using packages from tidyverse, here is an example:
# example dataset with rownames
a <- mtcars[1:3, 1:3]
a
# mpg cyl disp
# Mazda RX4 21.0 6 160
# Mazda RX4 Wag 21.0 6 160
... | biostars | {"uid": 303025, "view_count": 14562, "vote_count": 3} |
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... | depending on what you're looking for, like simple counts for instance, awk/perl solutions could be enough. if you need a deeper description, `bcftools stats` would give you some interesting details.
if your 2 samples are in a single vcf file I would suggest to split them first
bcftools view -Oz -c1 -s sample1... | biostars | {"uid": 224919, "view_count": 16415, "vote_count": 14} |
**Can I transfer this first format to the second one just by basic shell procession or awk or sed on linux? This is a toy example:**
This kind of text file is what I have, three cols, col2 and col3 like range, left close and right open,
chr1 0 2 0
chr1 2 6 1.5
chr2 0 3 0
chr2 3 10 2.1
Transfer... | awk '{B=int($2);E=int($3);for(i=B;i<E;++i) printf("%s\t%d\t%s\n",$1,i,$4);}' in.bed | biostars | {"uid": 325861, "view_count": 1209, "vote_count": 1} |
I need to calculate the median in the fastq file, how can I do this with awk or bioawk? | Straight up `awk` soliution would be:
cat *.fq | awk 'NR % 4 == 0 { print length($1) } ' | awk ' { a[i++]=$1; } END { print a[int(i/2)]; }'
I would do it with `bioawk` and `datamash`
cat *.fq | bioawk -c fastx '{ print(length($seq)) }' | datamash median 1
you can also implement a better median in awk as... | biostars | {"uid": 9496524, "view_count": 900, "vote_count": 1} |
Hi Everyone,
We have commissioned RNA-seq and analysis by a company, which provided us with raw fastq files, BAM files, and a count matrix. They used hard clipping and Tophat for the alignment to GRCm38/Mm10. I have attempted to recreate their analysis with HISAT2 (same reference genome), using simply the default pa... | Apparently, this problem is inherent to IGV. When we ran the same files that showed no reads on a different operating system, everything looked just fine. There are, of course, still differences between the Tophat and the HISAT2 alignments, but nothing is missing altogether. I will try to switch to the UCSC Genome Brow... | biostars | {"uid": 309059, "view_count": 1788, "vote_count": 1} |
Hello All,
I have read counts from RNA seq data in row and columns. I want to quantile normalized them in R. I have following code. This gives me the normalized values. However, the output is a matrix. I want the output with row name and column name so that I can perform PCA on it.
data <- read.csv("data.... | Try this (note the extra line; also use `data.matrix`, not `as.matrix`):
data <- read.csv("data.csv",header=T)
head(data)
rownames(data) <- data[,1]
data_mat <- data.matrix(data[,-1])
head(data_mat)
data_norm <- normalize.quantiles(data_mat, copy = TRUE)
| biostars | {"uid": 296992, "view_count": 15080, "vote_count": 4} |
So I'm trying to understand the --shift and --extsize parameters in MACS2. I have inherited an ATAC-seq that used the following MACS2 command.
macs2 callpeak -t ATAC_sample-1.bam --nomodel --shift -100 --extsize 200 -g 1.5e9 -f BAM
I'm trying to see how I can apply these principles to a Rscript I have that... | You'll need to `endoapply()` a function that does the `shift()` according to the strand, since that's otherwise ignored. Then `resize(aln, 200)`. Alternatively, use `idx = which(strand(aln) == '+')` for each strand and directly adjust the start accordingly (then `resize()`). | biostars | {"uid": 207318, "view_count": 13697, "vote_count": 3} |
Hello,
I have microarray data from the chip [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], and I am trying to annotate the probe IDs in R using the hugene10sttranscriptcluster.db package and the following function:
annotatedTopTable <- function(topTab, anotPackage)
{
top... |
Yes, for most use-cases, that package is correct. It will depend on how the original array data was processed.
You only need to do this, by the way:
require(hugene10sttranscriptcluster.db)
mapIds(
hugene10sttranscriptcluster.db,
keys = probes,
column = 'SYMBOL',
keytype = 'P... | biostars | {"uid": 9485622, "view_count": 1024, "vote_count": 1} |
Hi folks:
I am trying to get raw RNASeq data from ENA and wonder how to know the length of the sequences in those FASTQ files without downloading them?
In the query design I follow their [guide][1], and use the "`nominal_length>XXX"` in the query, but this filtering mechanism doesn't work...
Thanks!
[1]: http://ww... | Get the count of total bases and number of reads from ENA, and do below calculation,
Read length = Total Bases/ number of reads | biostars | {"uid": 133763, "view_count": 2382, "vote_count": 1} |
<p>I want to find the coordinates of all occurrences of the sequence recognized by a restriction enzyme. I know that using EMBOSS I may do this, but this task seems perfectly fitted for short-read sequence alignment software. However, I didn't find any reference for this.</p>
<p>I used bwa for the task and quickly obt... | Here is an update for people landing on this question: The bwa method that I proposed does not work properly. I don't remember exactly why it was wrong but I stop using it. I think it was returning regions with NNNs.
My solution was to use Biopython to search for a pattern. This is quite fast and accurate. Here is t... | biostars | {"uid": 17968, "view_count": 4233, "vote_count": 2} |
Hello all,
I am looking at the Level 3 CNV files on TCGA - the ones generated using SNP microarrays. I have a few questions:
1. How is 'segment mean' calculated and what is the exact biological interpretation?
2. For each patient I have two files called e.g. `....hg19.seg.txt` and `...nocnv_hg19.seg.txt`. What does e... | [Here][1] is the best documentation (that I know of) for TCGA SNP-array based CNV data. Regd. your two questions:
1. CBS segmentation algorithm identifies regions in the genome that, in spite of noise, probably have a uniform underlying copy number. The "segment mean" of each region is reported in the level 3 file, an... | biostars | {"uid": 111417, "view_count": 10491, "vote_count": 5} |
Hi,
I wanted to download 10 abstracts for 10 specific mouse genes (for a total of 100 abstracts). I was thinking of searching Pubmed for it, so I put in my first gene (FOS) in the search bar. But there was no option (that I could find) for mentioning the species I want to restrict my search to. So the results were e... | This thread piqued my interest since I wanted to write a script to do this for a web app. I'm not sure why the above examples don't work but here's how I got it going.
First you need the gene ID for Fos. You can do that just by searching:
https://www.ncbi.nlm.nih.gov/gene/14281
The Gene ID is the number at the e... | biostars | {"uid": 250368, "view_count": 1338, "vote_count": 1} |
I've got a bam file of paired-end illumina sequences mapped to a reference sequence and I was wondering if when I call the samtools view command if the results represent only reads that completely span over the region of interest or if it also included reads that intersect it by one or two base pairs.
If not are th... | [bedtools intersect][1] with -f 1.0 or -F 1.0 should do what you want. Something like:
bedtools intersect -F 1.0 -a intervarls.bed -b file.bam
I am not an expert on bedtools, though, so you may have to tweak / correct this command.
[1]: http://bedtools.readthedocs.io/en/latest/content/tools/intersect.htm... | biostars | {"uid": 308021, "view_count": 2181, "vote_count": 1} |
Hello,
I am looking at the human genome available through Bioconductor packages: NCBI GRCh38 and UCSC.hg19. And I do not get all the different sequence names I see. Could you help please?
In the UCSC.hg19, I do have chromosomes 1 to 22 + X and Y. But I also have chrM, chr1_gl000191_random, chr4_ctg9_hap1, chrUn_gl000... | chrM == MT == mitochondrial DNA. You should probably use this.
The `chrUn_*` sequences are unplaced contigs. So they may belong in the genome, but we don't know where. I personally use these, but I know that's not universal.
`chr*_unlocalized` and `chr??_*_random` are contigs that are known to belong to a specific ch... | biostars | {"uid": 114335, "view_count": 1634, "vote_count": 2} |
Hello everyone,
I would like to know if there are tools that feeded with ChIP-seq data for various histone marks, identify the enhancers by the "right" methylation/acetylation combinations.
Until now, I found CSI-ANN, but I was wondering if there are other tools.
Thanks
| The search term you're looking for is "chromatin segmentation". For example, omicstools has [a list of chromatin segmentation tools][1]
Of these, [ChromHMM][2] is probably the most widely used in publications at the moment.
Also see other answers on biostars on chromatin segmentation and enhancers:
- https://... | biostars | {"uid": 200697, "view_count": 3393, "vote_count": 1} |
Hi everyone,
I would be very grateful if you could help me.
I want to download the sequences of all the exons for each human gene. I went to ensembl biomart and tried to do it for BRCA2 first (this was a random choice). First I selected the following attributes: Unspliced(gene), Exon start, Exon end, strand, Gene... | Download refGene.txt.gz from UCSC :
wget http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz
Then keep only uniq Gene name ( column 13 ) and extract coordinate ( chrom - exonstart - exonend) to a bed file. Column 10 and 11 contains exonsStart and exonEnd position separated by a comma.
... | biostars | {"uid": 218009, "view_count": 3310, "vote_count": 1} |
Hello All,
I am confused about RA-seq normalization methods and when is appropriate to use them. I appreciate if you could share your thought with me.
My understanding from TMM and TPM is that TMM is appropriate for between sample/condition comparison as it counts for RNA composition in addition to library size ... | Online tools use TPMs for illustration because they can calculate them once and be done. This is convenient when people want to add samples over time and change groups and samples being visually compared. The results of that will not be as robust to outliers as normalized counts (produced with TMM or another method), b... | biostars | {"uid": 317417, "view_count": 13590, "vote_count": 6} |
Dear community,
I ran phyml on a gene family to build a tree. Looking at the results, I'm a bit worried about the log-likelihood value: it's -754, which means the likelihood is almost zero! Does this mean that the program has little confidence in the estimated parameters or the tree topology? I was wondering if I'm... | The principle of maximum likelihood is to choose the tree which makes the data most probable. As tree probabilities are usually tiny, especially for large datasets, we express them as ln(P), which is the log likelihood (LL). LL is a negative number (log function is negative in the 0-1 range), and the best it can be is ... | biostars | {"uid": 9513570, "view_count": 510, "vote_count": 1} |
Hi community!,
I'm annotating variants with the VEP software and I'm finding some unexpected transcript data of the type:
- NM_014938.4_dupl16
- NM_001170637.2_dupl3
```
1 206516261 . C T 47 PASS CSQ=T|non_coding_transcript_exon_variant|MODIFIER|SRGAP2|23380|Transcript|... | We are investigating these. It looks like some RefSeq transcripts (eg NM_001170637.3) have been duplicated in Ensembl's other_features database with a lower version number and this dupl suffix (eg NM_001170637.2_dupl3). This has been propagated across to the VEP cache, which is why you're seeing them. We don't currentl... | biostars | {"uid": 312593, "view_count": 1677, "vote_count": 2} |
<p>One of our project used to query OMIM data as XML through NCBI's efetch utility, as described here for example:</p>
<p><a href="http://biostar.stackexchange.com/questions/4194/what-is-the-best-way-to-interact-programmatically-with-omim">What is the best way to interact programmatically with OMIM?</a></p>
<p>Howeve... | <p>FYI: this was just announced this morning via twitter:</p>
<p><a href="https://twitter.com/#!/OmimOrg/status/196939511220015104">https://twitter.com/#!/OmimOrg/status/196939511220015104</a></p>
<blockquote>
<p>@OmimOrg</p>
<p>OMIM API is now open, see <a href="http://omim.org/api">http://omim.org/api</a> an... | biostars | {"uid": 19421, "view_count": 5967, "vote_count": 5} |
Hi guys,
I have an R programming question. I want to compare the genotype (`.GT` columns) with the given alleles (`.allele` columns) in dataframe `df1` and see if they are concordant or not. The rule is that if there is only one allele, it should be 0/0. If there are two alleles (for example GA), the genotype should b... | Data:
```r
df <- data.frame(allele1=c("A","AT","C"),GT1=c("0/0","0/0","0/0"),
allele2=c("AT","G","CG"),GT2=c("0/0","0/0","0/0"))
```
First I create a vector of correct translation. But I am assuming that there is always a 0/1, never a 1/0:
```r
library(stringr)
translation <- function(x) ifelse(str_length(df[,x])>1,... | biostars | {"uid": 141869, "view_count": 3865, "vote_count": 5} |
Dear all
I followed some links here in biostar to get the differential expressions of my RNAseq data for tumor vs control.
Then I get the pathways, I did somatic mutations using GATK pipeline to get some somatic mutations.
I found some differentially expressed genes and found common somatic mutations in them, c... |
Just some ideas off the top of my head:
1. **Mutation-to-expression modelling:** For each mutation, test it's association to the expression of
differentially expressed genes (DEGs) in the mutation's 'vicinity'.
This can be as easy as building a linear regression model with
expression as the *y* (de... | biostars | {"uid": 314312, "view_count": 890, "vote_count": 1} |
scRNA-seq novice here: We have four 10X scRNA-seq samples (wildtype and knockout condition) as n=2 each.
Each pair (so one WT and one KO) was produced on the same day respectively, same FACS sorting machine, same lab, same technician etc, so avoiding batch effects as much as we could.
For comparative analysis betwe... | I would apply the mutual nearest neighbours correction for the exact reasons laid out by the developer here: https://osca.bioconductor.org/multi-sample-comparisons.html#sacrificing-differences | biostars | {"uid": 437572, "view_count": 2517, "vote_count": 2} |
> The denominator of this expression can be interpreted as a pseudo-reference sample obtained by taking the geometric mean across samples. Thus, each size factor estimate sˆj is computed as the median of the ratios of the j-th sample's counts to those of the pseudo-reference.
But what if there are zero counts? The geo... | <p>if a gene has 0 counts in one sample, it is <a href="https://github.com/Bioconductor-mirror/DESeq2/blob/release-3.1/man/estimateSizeFactorsForMatrix.Rd">excluded</a> from this computation. this is not the ideal solution, but usually the number of genes that have some counts in all samples is so high that the estimat... | biostars | {"uid": 161162, "view_count": 2863, "vote_count": 2} |
<p>Hello all,</p>
<p>I have a very large list of NCBI gene IDs (such as, gi:47221249, ect). I am hoping to use this list to get the descriptions for each of the gene IDs. Using the GI above it would be "unnamed protein product [Tetraodon nigroviridis]".</p>
<p>Thus ending up with a file that has two col... | With <a href="http://www.ncbi.nlm.nih.gov/books/NBK179288/">Entrez Direct</a> you can:
efetch -id 47221249 -db protein -format docsum | xtract -element Title
unnamed protein product [Tetraodon nigroviridis]
Or if you have Blast installed you could fetch latest nr and query it with `blastdbcmd`. | biostars | {"uid": 110000, "view_count": 11500, "vote_count": 1} |
Hi all,
While working on a ChIP-Seq data set consisting out of 16 samples I want to see the differences in peak height. To achieve this I first need a merged peak location. To achieve this I was thinking of a tool which could merge all 16 of my peak files at once. E.G. bedtools merge / multiinter. Only thing is that I... | This should do it, concatenate peak locations in all peaks, sort them and merge
cat A B C .... | sort -k1,1 -k2,2n | mergeBed -i stdin > locations.bed
To know which files the peaks co-ordinates are merged from, you need to have an identifier in each file before merging.
Use
awk '{print $0"\t","peakFile-"NR}... | biostars | {"uid": 144369, "view_count": 7761, "vote_count": 1} |
Hi,
I am working on an assembly of a genome and currently am trying to annotate and visualize the regions of consecutive Ns. I would like to see the regions of my newly assembled genome, that are gaps (NNNNn) .
The way i tried to do it is with Letterfrequencyinslidingwindow command of Biostrings, but it takes f... | Try something like this using the Biostrings Bioconductor package.
```
library(Biostrings)
x = DNAString("ACTGNNTTGGNNNNAACTGC")
y = maskMotif(x,'N')
z = as(gaps(y),"Views")
ranges(z)
as.data.frame(ranges(z))
```
The final output from above will be:
```
start end width
1 5 6 2
2 11 14... | biostars | {"uid": 305785, "view_count": 1314, "vote_count": 1} |
Hi,
I have received fastq files containing the reads from Illumina MiSeq. Since they are paired-end, there is an R1 and an R2 file for each sample. So I expected to find reads beginning with our forward primer in the R1 files, and reads beginning with our reverse primer in the R2 (or vice versa). However, I find both ... | Actually the reads are always mixed just the way you describe them. R1 may be forward or reverse. R2 may also be forward or reverse. You are only guaranteed that the pairs are complementary.
Depending on your requirements, you may indeed need to check which is which down the pipeline. Standard alignment utilities do ... | biostars | {"uid": 244732, "view_count": 11651, "vote_count": 1} |
Duplicate reads have first been removed using picard:
java -jar -Xmx3g picard/dist/picard.jar MarkDuplicates INPUT=input.bam OUTPUT=output.bam METRICS_FILE=output.dup_metrics CREATE_INDEX=TRUE VALIDATION_STRINGENCY=SILENT
When I run samtools flagstat on the output bamfile I get the following:
2182812 +... | Picard `MarkDuplicates` *marks* duplicates, rather than removing them. Instead, when it finds a duplicate read it sets the duplicate flag to true and then outputs it. To remove the duplicates you need to add
REMOVE_DUPLICATES=true
to the command line. | biostars | {"uid": 208897, "view_count": 10981, "vote_count": 2} |
Hi everyone!
Sorry for this noob question, but I just wanted to ask, what is the best practice in the field for publishing RNA sequencing data analysis scripts? Does it usually happen before the publication, or after? Currently I kept the repo as private and the paper is not published yet. | Generally, it doesn't really matter unless you're publishing a custom, novel method where the code is really an integral part of the publication. In such a case, you'd want to keep it private until publication. Otherwise, keeping your random DESeq2 scripts in a public repo isn't going to hurt you or draw much attention... | biostars | {"uid": 9479724, "view_count": 815, "vote_count": 2} |
i have been trying to merge some ped/map files. i had removed or renamed the duplicated in the map file so i no longer get a duplication warning.
/home/chrystalla/plink-1.07-x86_64/plink --bfile snp_exc_1 --merge snp_exc_2.map snp_exc_2.ped --make-bed --out lets_merge
ERROR: Problem with MAP file line:
F102 PN1... | The MAP line generated in the error looks like a PED line. Either your files (.map .ped) are named incorrectly, or you need to change the order you read them into PLINK.
Your FID and IID should be alphanumeric. Removing the '-' may help? | biostars | {"uid": 232378, "view_count": 2882, "vote_count": 1} |
<p>I want to split my bam file into paired aligned reads and unpaired aligned reads for a much easier downstream analysis.</p>
<p>1) Is this possible to do in one run through the file with samtools?</p>
<p>2) If this is not possible with samtools directly, is it possible with the pysam wrapper library?</p>
<p>... | <pre>
samtools view -f 4 -o umapped.bam -U mapped.bam in.bam</pre>
<p>http://www.htslib.org/doc/samtools-1.1.html</p>
<p>"-U FILE Write alignments that are <em>not</em> selected by the various filter options to <em>FILE</em>. When this option is used, all alignments (or all alignments intersecting the <em>r... | biostars | {"uid": 138662, "view_count": 1772, "vote_count": 1} |
My goal is to make PCA and correlation plots of my RNA-Seq BAM files. Some useful discussion on BioStars such as [this][1], have helped guide my steps.
In another post, responding to a question on library size normalization at this BioStars [post][2], user [ATpoint][3] indicates size factor calculation must be perf... | Please use `1/calcNormFactors(object = raw.count)` as the scaling factor. Whether you use TMM or the default RLE is largely immaterial to me. Your `bamCoverage` command looks fine. | biostars | {"uid": 452905, "view_count": 1761, "vote_count": 2} |
Hi All,
I have a question regarding adapter trimming process of small RNA-seq data. The library for this dataset was prepared using NEBNext multiplex small RNA sample prep set for illumina (E7300S/L: https://www.neb.com/-/media/catalog/datacards-or-manuals/manuale7300.pdf). So I used `bbduk.sh` from BBtools(https://jg... | Hi:
I'm one of the developers of the NEBNext kits.
The reads you show seem to contain the sequence of the 3' adapter as expected for small RNA.
The 5' adapter sequence begins with a G (no A-tailing for this library type). The 5' adapter sequence should not be found in read 1, and I don't see it in the sequences y... | biostars | {"uid": 327802, "view_count": 4500, "vote_count": 2} |
<p>Dear lazyweb,</p>
<p>I wonder how data are stored behind the <strong>Exac</strong> server http://exac.broadinstitute.org/ :</p>
<ul>
<li>SQL only ?</li>
<li>SQL+tabix/VCF ?</li>
<li>Gemini ?</li>
<li>...</li>
</ul>
<p>Thanks.</p>
<p>Pierre</p>
| <p>Pierre;</p>
<p>The source code is here:</p>
<p>https://github.com/konradjk/exac_browser</p>
<p>It looks like a MongoDB database and Python Flask webserver. It also builds on xBrowse:</p>
<p>https://github.com/xbrowse/xbrowse</p>
| biostars | {"uid": 129818, "view_count": 6727, "vote_count": 3} |
<p>Dear All,</p>
<p>I am using <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> files for chip-seq analysis. The chromosome notation in a usual <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> file is like: chr1. In my file the chromosomme notation is 1. Is there a way to change that in the <a hre... | Edit: ~10 years later.
Some options:
**1)** See I wrote http://lindenb.github.io/jvarkit/ConvertBamChromosomes.html
**2)** You can use `samtools view` to dump your data with the header: http://samtools.sourceforge.net/samtools.shtml and replace the chromosomes with `sed` or `awk`. (**not tested** but it could be som... | biostars | {"uid": 13462, "view_count": 37716, "vote_count": 15} |
I have two fasta files, with the same headers/names for the sequences but different sequences.
I would like to combine them into one file, so that each sequence has the same name but is a combination of both sequences.
My preferred language is bash script, but I'm open to other suggestions.
thanks. | assuming there are only twho lines per sequence (title/dna) and they are ordered the same way.
paste f1.fa f2.fa | sed -e 's/\t>.*//' -e 's/\t//' | biostars | {"uid": 231806, "view_count": 8418, "vote_count": 2} |
Hello All,
I have a large set of genes with differential expression p-values (from DEseq2) and directional (up or down-regulated) information. I was wondering if anyone knew of a pathway enrichment analysis program that could make use of all of this information rather than just the gene list? Sorry if I have missed ... | There is a nice review in [Plos Comp][1] about the different methods that are available for pathway of GO analysis. The methods (with only a list of significant genes) you are referring to are first generation. There are also second and even third generation. Read it in the paper, and you'll know what to look for.
... | biostars | {"uid": 321269, "view_count": 1448, "vote_count": 1} |
Hello All,
Our lab is getting some interesting results whereby we have modules that have both positive and negative kme values in a signed network. If a higher power is used this goes away but the lower power already surpasses the R2 and k.means thresholds. Any insight would be helpful.
Best,
Duc | Thanks Kevin and all who have looked at this issue-- Peter Langfelder suggested bypassing use of TOM for the dissimilarity metric used to cluster, which can disagree sometimes substantially with expected module membership based on kME table (based on the experience with this and similar large multi-batch, batch-correct... | biostars | {"uid": 339326, "view_count": 3754, "vote_count": 1} |
I may be missing something in the html help page, but is there a way not to have any labels aside from changing the label size to 0? Thanks. | Sorry, I should have made this more intuitive. You just need to do:
lab = NA
Kevin
| biostars | {"uid": 415803, "view_count": 7442, "vote_count": 2} |
I would like to use regular expressions to identify a motif in an amino acid sequence. Part of the the motif is described as '2 or more out of XXXX are D or E'. I wonder if there is a way to specify this part directly with regular expressions instead of writing out all the alternatives or using a more iterative approac... | <p>I think I've figured it out now, using lookahead <code>(?=pattern) </code>to link two regular expressions like an <code>AND</code>:</p>
<p><s><code>(?=.?[DE]{1,4}.?[DE]{1,2}.?).{4}</code></s></p>
<p>The first part (in brackets) stipulates the pattern described by the following part must have at least 2 Ds ... | biostars | {"uid": 104868, "view_count": 2412, "vote_count": 1} |
Hi all,
Is there an API somewhere for fetching lists of accession numbers from NCBI that match some search criteria?
Context: I'd like to use their SRA Toolkit's 'prefetch' functionality (http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.The_SRA_Toolkit) to grab a bunch of sra files as part of a larger ... | <p>You mean like <a href="http://www.ncbi.nlm.nih.gov/books/NBK179288/">Entrez Direct</a> or the less user friendly <a href="http://www.ncbi.nlm.nih.gov/books/NBK25501/">eUtils</a>?</p>
| biostars | {"uid": 106842, "view_count": 2621, "vote_count": 1} |
I am looking for a tool/script/pony to correct the REF column in a vcf file whenever that nucleotide doesn't match the reference genome, as supplied in fasta format.
It sounds like a common task but I could not find something. I did find `bcftools +fixref` but that only works for SNPs. My vcf files are from structur... | This is the python solution I came up with, using cyvcf (minimally requiring v0.10.2) and pyfaidx. It can use compressed vcf and fasta files.
https://gist.github.com/wdecoster/d7fa440a74afd4607bb321ae0986fccd | biostars | {"uid": 347588, "view_count": 3945, "vote_count": 2} |
Hi all,
I'm looking for a simple solution for renaming fasta headers.
I have this fasta header
>trpE___AA_HMM___6fa05435949258489b608db9e58e5ba38821f2f26fffe5755daff43abin_id:MALBOS1|source:AA_HMM|e_value:5.2e99|contig:MALBOS1_000000117228|gene_callers_id:113772|start:215745|stop:217260|length:1515
And I would l... | Here's a solution using cut:
cut -d '|' -f 4 start.fasta | sed 's/contig:/>/' > end.fasta
| biostars | {"uid": 9546056, "view_count": 562, "vote_count": 1} |
Hi all,
I've just written a tool adding one or more **extra column** in a [VCF file](http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf3.3). The header now looks like this:
(...)
#CHROM POS ID REF ALT QUAL FILTER INFO MY_COL1 MY_COL2 FORMAT NA00001 NA00002 ... | Instead of inserting new columns which will screw up most tools, you should add your custom information at the **ANNO** column. This is what that field is designed for. With perl, it is very easy to extract the key-value pair there, e.g.:
perl -ane 'print "MYKEY=$1\n" if $F[7]=~/MYKEY=([^;]+)/'
Furthermore, VCF ... | biostars | {"uid": 994, "view_count": 7396, "vote_count": 2} |
Dear all,
I have pair-end RNA-seq data (Illumina) from parasite and I would like to do De-Novo assembly by TRINITY. I have reference genome of my host organism so I can map my data to host and remove from fastq contaminations.
My plan is:
1. Map with bwa/bowtie/novoaling my pair-end FASTQ files to a host reference g... | If you would like a Galaxy solution, this filters by ID: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id / https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id
This filters using a SAM/BAM mapping file: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping / https://testtool... | biostars | {"uid": 120756, "view_count": 5773, "vote_count": 1} |
Greetings,
I'm trying to get a sense of what people are using for local assembly. Ideally I'm looking for a tool that takes a BAM file and outputs a fasta for a region of interest.
EDIT:
I'm working with whole genome data. | Look no further than [Scalpel][1].
I've hacked out [the microassembler component of scalpel][2]. It does basically what you're describing except it produces an assembly graph from the BAM file in a particular region.
[1]: http://scalpel.sourceforge.net/
[2]: https://github.com/ekg/microassembler | biostars | {"uid": 126886, "view_count": 1967, "vote_count": 3} |
Dear all,
I am trying to install [Primer3][1] on an Ubuntu machine. Following the instructions, I moved into primer3-<release>/src and typed `make all` but i got:
/usr/local/lib/primer3/src$ make all
g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 primer3_boulder_main.c
g++ -c -g -Wall -D__USE_FIXE... | I finally was able to install it following the instructions in the github page here https://github.com/primer3-org/primer3
Installing
sudo apt-get install -y build-essential g++ cmake git-all
git clone https://github.com/primer3-org/primer3.git primer3
cd primer3/src
make
make test | biostars | {"uid": 306358, "view_count": 3731, "vote_count": 1} |
As the title says, Discovar De Novo (52488 - I think this is some version identifier) keeps saying that it can't allocate memory - it then reliably aborts. This is driving me up the wall because I'm queueing often for days for access to a 1 Tb compute node on the HPC.
**The details of my sequencing data:**
-----... | For anyone looking at this post, who has the same problem: I have it fixed now.
I was pointed at a forked version of Discovar, developed by a group at the Earlham Institute in Norwich. They wanted to use Discovar De Novo to assemble a wheat genome and it just crashed, so they got into it and fiddled about and seem ... | biostars | {"uid": 267292, "view_count": 2449, "vote_count": 1} |
I have a bed file called `my.bed` with CHROM, START, and END Position. Can someone please explain me how I can use bcftools or command to extract the regions from `myvcf.vcf` file? | my preferred option when dealing with vcf files is [bcftools][1], which requires vcf indexing:
tabix -p vcf my.vcf
bcftools view -R my.bed my.vcf.gz
another perfectly valid alternative, as Devon has just pointed out, would be [bedtools intersect][2]:
bedtools intersect -a my.vcf -b my.bed
[... | biostars | {"uid": 188137, "view_count": 14552, "vote_count": 1} |
Hello,
I am trying to get haplotypes for one locus on chromosome19 and for that, I need phased data. However, prior to the phasing, I am supposed to split my PLINK files into separated files by chromosome. I found this script online but it doesn't work (see below). Can you please give me advice on how to do this? I ... | I think the correct format is (in case some codes are commented out):
```
#!/usr/bin/perl
# This script takes as input the base filename of binary pedfiles (*.bed,
# *.bim, *.fam) and a base output filename and splits up a dataset by
# chromosome. Useful for imputing to 1000 genomes.
chomp( my $pwd = `pwd` ... | biostars | {"uid": 387132, "view_count": 7421, "vote_count": 2} |
Hi everyone,
My lab is using gene expression data generated by Illumina Human HT-12 v3 Expression Beadchips. As advertised by the company, this products has 48000+ probes for 25000 genes. I have never used expression data before and would like to cluster genes based on their expression. The data has already been norma... | Hi,
Its easier to do this in R. All you need is to convert ProbeID into the Gene name to which it is mapped.
```
> probeID=c("ILMN_1690170", "ILMN_2410826", "ILMN_1675640", "ILMN_1801246",
"ILMN_1658247", "ILMN_1740938", "ILMN_1657871", "ILMN_1769520",
"ILMN_1778401")
> library("illuminaHumanv4.db... | biostars | {"uid": 109248, "view_count": 17710, "vote_count": 2} |
Dear All,
I have a big embl file that has over 1000 IDs, and I want to split it based on IDs. Each ID should be a separate file containing all information of related ID, and should have the ID name.
How to do that?
| @OP: please post first embl record for better parsing.
Note: Before proceeding, create a test directory, copy the original embl (test.embl below) and run the script and check the output for random files.
OP embl ID line:
> ID scaffold00001; SV 1; linear; unassigned DNA; STD; UNC; 6279 BP.
based on OP ID... | biostars | {"uid": 280114, "view_count": 1782, "vote_count": 1} |
Hello, I am wondering, what tool/R-package can be used to draw this type of tree (preferably, programmatically)?
![enter image description here][1]
The image is taken from: https://www.ncbi.nlm.nih.gov/pubmed/26773003
[1]: http://ivanya.com/tmp/2016/1024.tree.png | Now it is supported by [ggtree](https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/).
| biostars | {"uid": 218591, "view_count": 3073, "vote_count": 2} |
In Biostars forum for differential gene expression analysis by LIMMA I found that most people suggest to set a threshold value of Log2FC > or = 2 to filter DEGs. When I analyzed the GEO dataset "GSE90594" - Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 platform for DEGs by LIMMA package, I found that... | The fold change will tell you something of the size of the effect of differential expression, so it's more about biology than about statistics. If you are looking for genes with big changes, you'll pick a higher cut-off. But if a gene is significantly differentially expressed then it's already worth looking into it: su... | biostars | {"uid": 373655, "view_count": 17375, "vote_count": 3} |
I have RNA-seq data with 2 conditions and 3 replicates per conditions.
I ran the [New Tuxedo pipeline][1] and also created some [read count tables][2] with prepDE.
I analysed differentially expressed genes with `Ballgown` and `DESeq2`.
With a treshold of 1 log2FoldChange and 0.01 padj in `DESeq2`: 14400 /32000... | *pval* is the nominal p-value. *qval* is the adjusted p-value, which are also known as q-values (not many people know this).
Ballgown may be using FPKM data when conducting the differential expression analysis. FPKM is not suitable for this purpose. Please confirm the type of normalisation that you used in Ballgown.... | biostars | {"uid": 324916, "view_count": 3551, "vote_count": 1} |
Hi all, I am new to the BioInformatics, and quite a beginner in programming languages. Can anyone suggest me some sources where I can at least learn 50% of the scRNA seq data analysis? I am familiar with C language, and I know a little bit of molecular biology too. | Single-cell data are rather unpleasant as a beginner's topic due to the noisy and sparse nature of these data. Maybe better first analyze some bulk RNA-seq data to get familiar with R (see [here][1]), and then dive into the documentation of `Seurat` which is the jack-of-all-trades in terms of scRNA-seq analysis. For lo... | biostars | {"uid": 373386, "view_count": 4322, "vote_count": 7} |
Hello,
I don't know why I am getting some errors during my analysis
I uploaded an example of my data in
https://gist.github.com/anonymous/2c69ab500bfa94d0268a
I use the following command in R to load my data
data <- read.delim("path to your file /example.txt", header=FALSE)
however, in summary or head or othe... | Works perfectly for me:
```
> dat <- read.delim(file="Downloads/gist2c69ab500bfa94d0268a-ac4cd3d5b0d0764c2faae0e3fb0db8a39d75bb22/example.txt", row.names=1)
# your mistake was to set header=FALSE, and to omit
# row.names=1
> head(dat)
M1 M2 M3 M4 M5 M6 M7 M8 ... | biostars | {"uid": 130044, "view_count": 10954, "vote_count": 1} |
What exactly are RMA-units I get after normalizing affymetrix data?
These are relative expression log2 units. But relative to what? What is RMA = 0? | See this link to a presentation:
http://www.ub.edu/stat/docencia/bioinformatica/microarrays/ADM/slides/2_PreprocessingMicroarrayData-2-Preprocessing%20and%20Normalization.pdf
And also this link to some discussion on the topic:
https://www.researchgate.net/post/What_exactly_is_the_unit_of_measure_in_microarray_... | biostars | {"uid": 214013, "view_count": 8181, "vote_count": 1} |
Hi,
This appears to be a simple problem that I am unable to solve. I have some data that looks like this:
CHROM POS REF ALT TYPE AF
chr1 1 A T MISSENSE 0.23
chr2 1 A T,G MISSENSE 0.17, 0.09
The above is dummy meaningless data, but it is re... | You could use a Python script to do this easily:
#!/usr/bin/env python
import sys
headers = None
idx = 0
for line in sys.stdin:
elems = line.rstrip().split('\t')
if idx == 0:
headers = elems
sys.stdout.write(line)
else:
... | biostars | {"uid": 483199, "view_count": 770, "vote_count": 1} |
Hello everyone,
I am really new in this forum, so I hope you can help me in resolving my problem.
I am actually working on a project, where I have to annotate some sequences.these sequences are a result of rna_seq , and I have them in bam format. Do you know some easy bioinformatics tools that can help me to annnot... | OK, so you want to annotate (predict genes) on a genomic sequence making use of RNAseq info.
The question is easily asked but I'm afraid you might be underestimating how a complex matter this can be. But is absolute a good and correct approach. Problem is that this often requires quite a bit of work and knowledge. ... | biostars | {"uid": 371871, "view_count": 1840, "vote_count": 1} |
Hi,
I have been trying to use multiple command i can find online to spilt the columns into different files but couldnt.
I have an 10 columns excel file ( first 2 col is paramaters, the remaining 8 col is the data). I would like to split it into 8 separate files which all 8 contains first 2 col paramaters and 1 da... | Here is the code in R: Make sure that all for the files (excel files with .xls or .xlsx) are in the same format as in link furnished above (2nd column is mz, 5 is RT and 11th column onward samples). Code would create one excel file per sample and name of the excel file would be sample_"sample name".xls. It will have th... | biostars | {"uid": 326422, "view_count": 1495, "vote_count": 1} |
Hello, I am looking at this heatmap and I do not understand why some of the tumours are grouped with the controls, seems as if the heatmap is 'moved to the left':
Top of the heatmap:
![Top of the heatmap][1]
(it is a long heatmap so i upload just a section)
Bottom of the heatmap:
![Bottom of the heatmap][2]
... | There can be many reasons, some not really relating to bioinformatics:
1. these tumours genuinely exhibit the 'normal-like' methylation
profile over these probes
2. these tumours have normal cell contamination
Some informatics reasons:
- your coding is incorrect and you have incorrectly assigned a nor... | biostars | {"uid": 358231, "view_count": 1195, "vote_count": 2} |
How can we get total number of SNPs in plink association output file as "qassoc" and "adjusted file" which has less than 0.05
P values? | From the plink manuals the pvalue column for [qassoc file][1] is the 9th. So we can use `awk` to keep the 1st row header, then filter on 9th column value, see example:
awk '(NR==1) || ($9 < 0.05) ' myfile.qassoc > myfile_subset.qassoc
To get the number of rows:
awk '$9 < 0.05' myfile.qassoc | wc -l
... | biostars | {"uid": 331359, "view_count": 1726, "vote_count": 1} |
I am trying to convert a bigwig file to a wig file to run through sitepro. I tried using the ucsc tool bigWigToWig and I get a file that looks like this:
```
#bedGraph section chr1:0-3079820
chr1 0 3001030 0
chr1 3001030 3001060 2.41
chr1 3001060 3001230 4.83
chr1 3001230 3001270 2.... | <p>This guy experienced the same problem, and has an answer (and a script to go from bedGraph to wig) on his site:</p>
<p><a href="http://sebastienvigneau.wordpress.com/2014/01/10/bigwig-to-bedgraph-to-wig/">http://sebastienvigneau.wordpress.com/2014/01/10/bigwig-to-bedgraph-to-wig/</a></p>
| biostars | {"uid": 113824, "view_count": 4798, "vote_count": 2} |
Hey guys:
I am doing **RNA-seq** analysis and it seems that the quality of my reads is not desirable.
Below is **a typical fastqc report** for my data.
I have read many tutorial about fastqc, from my understanding, **it seems that the 1-10 bp are adaptor sequences**. But in the adaptor content section, there is... | The adapter starts at the 3' end of your reads, not the 5' (unless its an adapter dimer - i.e. no insert).
This is the result of random priming in RNA-Seq. I think [Biases in Illumina transcriptome sequencing caused by random hexamer priming][1] is the first paper on this. This represents real sequences. After align... | biostars | {"uid": 371979, "view_count": 6650, "vote_count": 1} |
Hi All,
I have a question regarding trimming of adapters in NGS data. I have previously analyzed RNAseq data using brtim (https://www.sciencedirect.com/science/article/pii/S0888754311001339) without using adapter sequence. I am now analyzing smallRNAseq data, and I am using adapter sequence as adapter.fa using BBduk.s... | One case is where there is a kit/prep specific adapter that is being used. This may require special handling of the downstream data based on the instructions included in the kit.
If you had paired end reads with enough pairs having short inserts then you can detect them by doing this: `bbmerge.sh in1=r1.fq in2=r2.fq... | biostars | {"uid": 329749, "view_count": 3142, "vote_count": 1} |
How to embed known cell information into Seurat object? Using AddMetaData?
Is this possible?
I read this documentation: https://www.rdocumentation.org/packages/Seurat/versions/3.1.4/topics/AddMetaData
However I need some clarification on how to go about doing this, please?
I have cell labels that are all al... | Hope I got your question correctly, you can do everything to cell information via `Ident` function. Follow the manual to change the `Idents` of your cells. By this, you can replace the `active.ident` with what you want.
| biostars | {"uid": 460935, "view_count": 24192, "vote_count": 1} |
**Hi everyone**
I would like to take a second opinion regarding a variant with DP =17. The variant is in a very high GC content area so the low coverage is reasonable.
I do hard filtering because I have few samples for VQSR, I thinks it is okay according to GATK hard filtering, the values are as follows:
... | I cannot provide a detailed answer given the information but a few comments.
There are 2 most likely models:
1) The site is homozygous reference
Therefore, the 3 reads are potentially a) mismapped, b) weird duplicates or c) sequencing errors.
a) Did you use a mappability filter? i recommend Heng Li's method ... | biostars | {"uid": 310806, "view_count": 1269, "vote_count": 2} |
Hi,
I've recently started using Ensembl for help in designing a gene panel for NGS.
Each time I select a gene on Ensembl it comes up with different available transcripts for that gene.
What defines a transcript? Is it literally just a different version of the gene in different individuals (but if so, how com... | This is more of a comment, possibly a rant. In my opinion the concept of gene is obsolete and we would be better off if we ditched the concept of "gene" altogether.
Genes made sense when it was thought that there were these discrete units (genes) which produced each a single transcript and a single protein. However... | biostars | {"uid": 244850, "view_count": 27920, "vote_count": 8} |
Hi All,
I have MiSeq PE250 reads for a viral vector sample. I trimmed the raw reads with Trim Galore (length >= 200 and Q >= 30). I aligned these reads using both `BWA MEM` and `Bowtie2 --local` and found a `AAA -> TTT` variant in both alignment files at different frequencies `9%` and `71%` respectively. I further a... | >The fastqc per base faultily fails for the super trimmed reads indicating a wrong Illumian Phred Score encoding version. Why did this happen?
Because with this line:
```
awk '{unit=unit $0 ORS} NR%4==0{if (/^[?@ABCDEFGHIJK]+$/) printf "%s", unit; unit=""}' trimmed.R1.fq > super_trimmed.R1.fq
```
you elimina... | biostars | {"uid": 372614, "view_count": 2109, "vote_count": 1} |
I have an ExpressionSet, combArr.eset, that contains Affymetrix Human Genome U133 Plus 2.0 Array gene expression data. I also have a matrix, exprs_combArr.eset, that contains the expression data for combArr.eset. The row names for exprs_combArr.eset are the hgu133plus2 probe IDs, and the column names are the Gene Expre... | Haha, this came up in a biofinormatics clinic I did on Friday. I've written a rather terse version of how to add gene-level annotations to an Affymetrix ExpressionSet [here][1]. You basically have to find an appropriate annotation package (probably hgu133plus2.db) and add that info to the featureData slot of your Expre... | biostars | {"uid": 254040, "view_count": 10389, "vote_count": 2} |
Hello,
I know the following question have been asked many times by now, but the suggested solutions were not helpful.
I have a set of taxIDs and I want to convert them to taxonomies, but I do not want to download any extra databases. Is there any simple way to do this via terminal?
| Another solution using [Entrez Direct][1]
efetch -db taxonomy -id 387462,2594474 -format xml | \
xtract -pattern Taxon -first TaxId -element Taxon -block "*/Taxon" \
-unless Rank -equals "no rank" -tab "," -sep "_" -element Rank,ScientificName
387462 superkingdom_Eukaryota,kingdom_Metazoa,phyl... | biostars | {"uid": 423201, "view_count": 3269, "vote_count": 1} |
Hi,
I encountered a strange issue while reading in a data table from `txt` format. If I read it from `txt` by `read.table` it does not include all rows but if I convert to `csv` and read it with `read.csv` its perfect. Does someone know the issue or is it my code?
[Here][1] is the file.
```r
test <- read.table("./... | Use the argument `quote = ""` inside read.table.
read.table("your_file", quote="", other.arguments)
**Explanation**:
Your data has a single quote on 59th line (`( pyridoxamine 5'-phosphate oxidase (predicted)`). Then there is another single quote, which complements the single quote on line 59, is on line 137... | biostars | {"uid": 221983, "view_count": 21347, "vote_count": 3} |
I have a genotype vcf file for which I want to do trimming such that I have one variant with MAF > 5% every 100kb.
Does anyone have suggestions to do this smartly using bcftools or vcftools ?
Thanks Kiran | using **VcfFilterJdk** http://lindenb.github.io/jvarkit/VcfFilterJdk.html
private String prevContig=null;
private int prevPos=-1;
private final int distance= 100_000;
public Object apply(final VariantContext variant) {
final double AF = variant.getAttributeAsDoubleList("AF",1.0).stream... | biostars | {"uid": 365303, "view_count": 938, "vote_count": 1} |
<p>I find the way to get the identity of hsp ,but no alignment.One alignment can have multiple hsp, that means the score(identity) of hsp is no equal to alignment. when i do blast in webpage, i always get scores and identities of alignments. Is that any logical problem i made, who can explain this?</p>
| <p>BLAST is a local alignment tool - it reports segments of the sequence, called HSPs, that align and produce the best scores. Each HSP in a match is a segment of query matching to a segment of the subject producing a high score. You can either use the meaningful maximum score or use a score totaled across all HSPs.</p... | biostars | {"uid": 118504, "view_count": 3508, "vote_count": 1} |
Hi, everyone,
As my title describes, where to download *Arabidopsis* gene expression data in batch? I know some sites, for example, eFP browser, AtGenExpress Visualization Tool (AVT), but they only browser one gene each time. I would like to get global gene expression map. Could anyone help? Thank you very much! | Hello biolab,
If you are thinking about array-based gene expression, you could download in batch at [Araport][1]. There are at least two ways to do so:
1. If you don't have a specific experiment in mind, use this pre-defined template (Click [Here][2]). You could select the expression values of a list of genes. There ... | biostars | {"uid": 157428, "view_count": 2386, "vote_count": 1} |
Hi,
I do have two groups of fastq files, I need to merge R1 reads of one file whose has same name at the beginning with the other R1 files reads.
Like Soil-13 is similar in two RI reads files,
I do have multiple pair-end read files like this that I need to merge into one. similarly, I need to do for R2 reads.
... | You can just concatenate them with cat:
cat Soil-13*_R1_*.fastq > Soil-13_R1_001.fastq
cat Soil-13*_R2_*.fastq > Soil-13_R2_001.fastq
etc.
You can generate a for loop to run through all libraries (bash):
for l in $(ls *_R1_*.fastq | cut -d "_" -f 1 |sort |uniq); do cat ${l}*_R1_*.fastq > ${... | biostars | {"uid": 371355, "view_count": 1976, "vote_count": 2} |
Assume we identify - by RNA-seq, tiling arrays, by prediction - possible candidate regions for non-coding, small RNAs. I wish to verify and predict the function of as many RNAs as possible by computation before going to the lab. One could use eg. Rfam to find similar sequences, after that we are left with more than 90%... | How are you doing your comparison to Rfam? If you're just running rfam_scan.pl or the CMs then this may not give you the results you really want. See the recent [paper by Kolbe & Eddy][1] to hear more about the limitations of CMs on truncated sequences. Could explain some of your lack of sensitivity vs Rfam. However th... | biostars | {"uid": 1662, "view_count": 6071, "vote_count": 12} |
Hi All,
I have a table with six columns (in the following).
![enter image description here][1]
[1]: http://uupload.ir/files/xm5g_taible.png
So, I want to delete SNPs that are less than number 10 in the SNP column.
What is the best idea?
Best Regard
Mostafa | awk !
a cmdline such as below one should do the trick:
awk ' $4 >= 10' <table-file> > new_file
and if you want to (additionally) apply calculations on a certain column:
awk ' $4 >= 10' <table-file> | awk '$2=$2+2000' > new_file
| biostars | {"uid": 337161, "view_count": 1292, "vote_count": 1} |
<p>I am writing a script to get SNP positions from dbSNP by using NCBI E-Utils. When I use esearch and efetch to retrieve the positions, I can only access positions from the newest genome build. Since I want to use GRCh37, this causes problem. I was wondering if you knew of a way of asking for a specific assembly in E-... | dbSNP does not support searches for older assembly coordinates.
Depending on exactly what you are trying to do, you can probably use lift-over or <a href="https://www.ncbi.nlm.nih.gov/genome/tools/remap">remap</a> to first convert your coordinates. | biostars | {"uid": 100566, "view_count": 1893, "vote_count": 1} |
Hello all,
I am new to RNA-seq, and would like your input to see if my results are real or not. I am trying to see if there are any differentially expressed genes between knockout and wild-type strain with 3 animals for each genotype. In my gene_exp.diff output from cuffdiff the most significant p-value is 5.00E-05 an... | <p>If I remember correctly, cuffdiff uses (in recent versions like yours) a kind of permutation test (<strong>edit</strong>: sampling procedure) to assess the significance of DE. This is why it has got "bins" of qvalues and the lowest one is still not so low. I'm anyway not sure of this.</p>
<p>Whateve... | biostars | {"uid": 175148, "view_count": 4273, "vote_count": 1} |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.