Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?

Question

[Hicham]

Hello,

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.

Answer 1

[dsull]

This looks like RSEM output.

Follow the instructions here: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#RSEM for the isoforms.results file.

[Hicham]

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.

[dsull]

You could set txOut=FALSE to get gene-level summaries.