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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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phyluce_assembly_match_contigs_to_probes #207

Closed quattrinia closed 3 years ago

quattrinia commented 3 years ago

Hi Brant, Is there a way to keep all loci that are thrown out as duplicates in the "finding UCE loci step"? I know you can keep a file of the dupes, but curious if you can actually just keep all loci? Or at least the contigs that match multiple loci.

Cheers, Andrea

brantfaircloth commented 3 years ago

Yes, there's a way... You can output the list of "duplicates" when matching loci, and then run that through https://gist.github.com/brantfaircloth/e48e7e4eb9748854962863d104f94095. YMMV and be careful with what you do with those duplicates loci!