DEseq2 · Biostar

DEseq2

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

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updated 2.3 years ago by Ram

• written 2.3 years ago by rrehimi •

1 answer

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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written 2.3 years ago by ATpoint

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