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mpc-bioinformatics / McQuaC

Transform the Quality Control workflow from Knime into a workflow in Nextflow
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Target/decoy-database #28

Open di-hardt opened 10 months ago

di-hardt commented 10 months ago

Hey,

I saw that the decoy generation is done by Comet. Parameter decoy_search = 1. I think, but correct me, Comet is using reverse decoys? Which is of course greate for reproducablitly, especially needed in a QC workflow, but lead to a higher overlap between target and decoys when I remember correctly.
Therefore I would like to to return to the previously used practise established at the MPC of using prebuild target/decoy databases where the decoys are shuffled. OpenMS does this very nice by keeping the cleavage sites in place, ensuring at least the same peptide lengths. Another advantage of prebuild target/decoy databases is timesaving, as the decoys are already present. Neglectable for one or two ISAs but for larger studies this could save some time.

Best, Dirk

Luxxii commented 1 month ago

We could do a flag (geenrate_decoy true | false) If set to false we could enforce that the user provides a specific format for decoas in the fasta header