Featurecounts countmatrix creation

Question

[Vikram]

Hello,

I have 15 BAM files, with 5 belonging to each of the control, treatment1, and treatment2 groups. I am wondering whether I should use all of the BAM files at once in the featureCounts command to create single count file for downstream analysis or if I should perform featureCounts on the individual BAM files separately. I am not sure if using all of the BAM files at once could cause any issues in downstream analysis such as differential expression analysis.

Thank you in advance!

Answer 1

[rpolicastro]

Running them all together is fine. It just puts all the counts into one file so it's slightly easier to import into e.g. R.