RSEM isoform.results outputs for edgeR
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12 months ago
weichengz • 0

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

rsem tximport edgeR • 893 views
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Entering edit mode
12 months ago

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

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12 months ago
igor 12k

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.

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