Question: summaries featureCounts output for egeR
0
gravatar for myprogramming2016
3.8 years ago by
myprogramming20160 wrote:

Hi,

I have used featurecounts to get read counts on my RNAseq libraries.

How can I compile results from different libraries for edgeR input? Is there any R package or perl script?

Thanks in advance your help.

YK 

edger featurecounts • 3.1k views
ADD COMMENTlink modified 3.8 years ago by Wei Shi3.2k • written 3.8 years ago by myprogramming20160
Answer: summaries featureCounts output for egeR
0
gravatar for Aaron Lun
3.8 years ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

You don't give any code indicating what you've already done, so it's hard to help - please read the posting guide when writing questions in future. Anyway, you should note that featureCounts can take a vector of BAM file paths, in which case the output will include a matrix of counts (genes = rows, columns = libraries). This can be directly used as input into edgeR. If you've already run featureCounts separately on each library, and you can't be bothered to run it again on all libraries, then you can just cbind the individual count matrices together into a single matrix for use in edgeR.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Aaron Lun25k
Answer: summaries featureCounts output for egeR
0
gravatar for myprogramming2016
3.8 years ago by
myprogramming20160 wrote:

Sorry! I did use linux commands to get read counts as follows.  

for i in *.sam;do featureCounts -p -T 5 -t exon -g gene_id -a genes.gtf -o $i.counts.txt $i;done

I have an output files as counts.txt for each of my library.

I can re-run featureCounts on R bioconductor. Could you please share an R code?

 

 

ADD COMMENTlink written 3.8 years ago by myprogramming20160

Or maybe you could just read the Rsubread documentation, or check out ?featureCounts.

ADD REPLYlink written 3.8 years ago by Aaron Lun25k
Answer: summaries featureCounts output for egeR
0
gravatar for Wei Shi
3.8 years ago by
Wei Shi3.2k
Australia
Wei Shi3.2k wrote:

For your linux command, you can include all your SAM files in one command and featureCounts will return you a file that includes counting results for all library.

If you use featureCounts in R, here is a case study you may find useful:

http://bioinf.wehi.edu.au/RNAseqCaseStudy/

 

ADD COMMENTlink written 3.8 years ago by Wei Shi3.2k
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