Using GeneCounts in DESeq2

[Shraddha Ranganathan]

Hi all, 

as a follow up to this thread, I'm wondering how to collate all the genecount files? 

I have 40 samples, and so I should receive 40 genecount files. If I'm going to use DESeq2 next, I should be able to input just one file for all 40 alignments, right? In this case, how can I combine all 40 files to give me one, featurecounts-esque file? 

Running DESeq2 40 times doesn't make sense, does it? 

thanks!
Shraddha

[Alexander Dobin]

Hi Shraddha,

first, you need to figure out which count column in the ReadsPerGene file is the right one according to the strandedness of the data.

Then you can cut this column from each file and paste the columns (together with the first gene name column) into one file that will be input for DEseq.

Cheers

Alex

[Shraddha Ranganathan]

Hi Alex, 
Makes sense, thanks for the response! That works just right