Hi,
There seems to be an issue with the QC report when using percolator as rescoring engine. When running the same files for percolator and mokapot, the QC report shows very big discrepancies. The reported PSMs and peptides in the logs for percolator also differ from the QC report.
These are the statistics with percolator:
The corresponding logs:
And these are the statistics for the same file with mokapot:
For another file, these are the statistics for percolator:
The corresponding logs:
And for the same file with mokapot:
Hi, There seems to be an issue with the QC report when using percolator as rescoring engine. When running the same files for percolator and mokapot, the QC report shows very big discrepancies. The reported PSMs and peptides in the logs for percolator also differ from the QC report.
These are the statistics with percolator:
The corresponding logs:
And these are the statistics for the same file with mokapot:
For another file, these are the statistics for percolator:
The corresponding logs:
And for the same file with mokapot:
Best, Justine