I have a peptide and I want to find whether this peptide has an expression in RNA-Seq data basically, I want to know the no of reads this peptide map to
Have you already mapped and annotated your RNA-Seq data? If so, grep (in bash or R) the name of your peptide and you will get that.
We believe that this post does not fit the main topic of this site.
OP did not follow-up. Please comment if this is still of interest.
For this reason we have closed your question. This allows us to keep the site focused
on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.