Entering edit mode
4 months ago
Hicham ▴ 10
I have a dataset contains the following columns: transcript_id, gene_id, length, effective_length, expected_count, TPM, FPKM, and IsoPct.
And for the same gene_id more than two transript_id .. so it's a transcript-level dataset
I thought I need to use tximport to convert it to counts so I could use it for DESeq2, but I didn't really get how can I convert it exactly.
Following the Rsem section of the tximport vigenettes ended by having a dataset of "transcripts" and "counts". still one critical step.. converting these transcripts to genes .. I'm more into gene-level.. but it's not the case as the same gene has multiple transcripts.
You could set
txOut=FALSEto get gene-level summaries.