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bzhanglab / PepQuery

PepQuery: a targeted peptide search engine
http://pepquery.org
GNU General Public License v3.0
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Are tags still supported or needed in PepQuery2 #43

Closed jj-umn closed 1 year ago

jj-umn commented 1 year ago

We have followed the procedure in: http://pepquery.org/data/PepQuery_for_immunopeptidomics_data.pdf for evaluating potential neoantigens using no-enzyme.
PepQuery2 does not have option: -tag Does the the index function in PepQuery2 replace the utility of the tags file?

wenbostar commented 1 year ago

The new version no longer needs tag file. But it will require larger memory for no-enzyme search compared with 1.x version and it is very likely to be slower than previous version. Please let me know if you have any additional questions for this function.

jj-umn commented 1 year ago

Thanks for the information.