We should probably add a check in the .fasta file processing to check for decoy prefixes when running a target-only search, and output a message with the below information if any are found.
If an external tool is used to create a target-decoy database with a specified prefix, by default users run a target-only search (because running a target-decoy search will often stop with an error when processing the database). This also means that MS-GF+ will not calculate QValues or PepQValues.
Instead of running a target-only search, they should instead do the following:
Make a copy of the .fasta file named [same name].revCat.fasta
Run the search with -tda 1.
What this does is bypass the MS-GF+ decoy creation process, while still performing a full target-decoy search.
We should probably add a check in the .fasta file processing to check for decoy prefixes when running a target-only search, and output a message with the below information if any are found.
If an external tool is used to create a target-decoy database with a specified prefix, by default users run a target-only search (because running a target-decoy search will often stop with an error when processing the database). This also means that MS-GF+ will not calculate QValues or PepQValues.
Instead of running a target-only search, they should instead do the following:
[same name].revCat.fasta-tda 1. What this does is bypass the MS-GF+ decoy creation process, while still performing a full target-decoy search.