Description
Hi,
I posted this question in an old thread about percolator-reset, but I did not get any response. I thought maybe my question was overlooked, because it was posted in an old thread, and so I decided to start a new one. If you already saw the question, sorry for reposting.
I have a question regarding Percolator-RESET. When I run it using this command:
percolator -Y --reset-algorithm --results-peptides peptides --results-psms psms --decoy-results-peptides decoy_peptides --decoy-results-psms decoy_psms pin.tab
one of the lines in the output states "Starting reset: psmsOnly" and indeed the resulting "peptides" file is empty. But when I look at the "psms" file I see only non-redundant peptides and q-values seem to have been calculated for peptides rather than psms. So, I am confused are these q-values for peptides or psms? If they are associated with psms, why are there no non-redundant peptides? Also, if the q-values are reported at the psms levels only, how do I get the q-values at the peptide level?
Thank you very much in advance for your help.