Tophat/Bowtie Not Using Gene Symbols From Gtf File

Question

[jobinv]

I have an issue with my RNA-seq analysis, and was wondering whether any of you know how to solve it? Basically, I want to be able to annotate my analysis with gene symbols. What I have done is to supply Tophat/Bowtie with a gtf file from Ensembl, which contains these gene symbols. However, instead of making use of these gene symbols (the column "gene_name" in the gtf file, for example "DDX11L1"), it seems to use the Ensembl gene ID's instead (the column "gene_id" in the gtf file, for example "ENSG00000223972").

How do I get Tophat/Bowtie to use the "gene_name" column instead? Is this possible?

Answer 1

[jobinv]

It seems I had been misunderstanding the setup of this for a while now. Precisely because each individual gene_name links to multiple gene_id's (because of for example multiple transcripts of the same gene), this cannot be done directly. It's better to rather annotate the transcripts to gene symbols at a later point during the downstream analysis, I've learnt.