RSEM isoform.results outputs for edgeR

Question

[weichengz]

I was hoping to quantify differential transcript expression (DTE) for my RNA-seq data. Following transcripts/isoform quantification using RSEM, I've got individual "sample_name.isoforms.results" files (column name below). I know that edgeR can work with expected counts as output by RSEM, but not sure how to process/prepare those files for edgeR. Any tips?

Many thanks, Wei

transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct

Answer 1

[swbarnes2]

You can use the expected counts, rounded. But does edger work with transcripts, as opposed to genes?

Answer 2

[igor]

Looks like you already have "tximport" as a tag. Have you checked the vignette? There are examples covering how to import RSEM output into tximport and then how to proceed with edgeR.