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 

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.

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?

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/