DEseq2
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5 weeks ago
rrehimi • 0

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

RNA-seq DESeq2 • 322 views
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Entering edit mode
5 weeks ago
ATpoint 82k

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.

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