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snijderlab / stitch

Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling
MIT License
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Use Nonselected Templates as Decoy #206

Closed kostrouc closed 1 year ago

kostrouc commented 1 year ago

Hi,

I noticed that in the publication it was mentioned that templates which don't match can be used as decoys. How is this parameter specified? Do we have to manually remove those that did not hit and place them in a fasta file? Is this the EnforceUnique parameter? I don't see it listed in the manual.

Thank you!

douweschulte commented 1 year ago

There is no need to do this manually the option is called Decoy in recombine: https://github.com/snijderlab/stitch/blob/master/BatchFiles.md#decoy-s. If you have any ideas to makes this more clear in the manual I am open to your feedback.