Question: RSEM isoform.results outputs for edgeR
0
gravatar for weichengz
4 months ago by
weichengz0
Melbourne, Australia
weichengz0 wrote:

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

edger rsem tximport • 346 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by weichengz0
0
gravatar for swbarnes2
4 months ago by
swbarnes29.2k
United States
swbarnes29.2k wrote:

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

ADD COMMENTlink written 4 months ago by swbarnes29.2k
0
gravatar for igor
4 months ago by
igor11k
United States
igor11k wrote:

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.

ADD COMMENTlink modified 4 months ago • written 4 months ago by igor11k
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