Hi all,

Regarding the package DESeq2,

-What are the input files? BAM/SAM files?

-Does it makes the counting and the differential expression analysis, or just the latter?

Thank you. Regards,

Carlos

You should read this RNA-seq workflow on f1000research, which describes how you get from raw reads to results.

To get you started, however, the DESeq2 workflow starts with the assumption that you already have a count matrix of read/fragment counts per gene for your samples of interest.