DEseq2

Question

[rrehimi]

Dear All,

For Deseq2, should I use feature counts files as input (treated vs control)? Should I include the Annotation.gff3 file as well, which I downloaded from the Gencode website?

Thanks in advance,
Rizwan

Answer 1

[ATpoint]

The DESeq2 input is a numeric count matrix (or data.frame) with rows being genes/observations and columns being samples/cells/specimen. Please see the DESeq2 manual. GFF files are no input.