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AppliedBioinformatics / runBNG

An easy way to run BioNano genomic analysis
MIT License
27 stars 7 forks source link

Enzymes #1

Closed yyx8671 closed 3 years ago

yyx8671 commented 7 years ago

Recently, BioNano Genomics has added 'BssSI' to their enzyme list. We provide two options to help users complete NGS reference sequences digestion.

splaisan commented 7 years ago

Thanks a lot for this fix. Maybe you could consider migrating to fully using github pull and help people update from a release repo upon reception of a mail from you.BestStephane

Sent from my smartphone. -------- Original message --------From: Andy Yuan notifications@github.com Date: 6/23/17 06:38 (GMT+01:00) To: AppliedBioinformatics/runBNG runBNG@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [AppliedBioinformatics/runBNG] Enzymes (#1) Recently, BioNano Genomics has added 'BssSI' to their enzyme list. We provide two options to help users complete NGS reference sequences digestion.

cmapMaker. py at https://github.com/AppliedBioinformatics/BioNanoScripts modify the original 'fa2cmap.pl' file under /path/to/BioNano scripts/HybridScaffold/scripts by adding:

"BssSI" => "CACGAG" on line 77 } elsif(uc(substr($opts{n}, 0, 4)) eq "BSSS"){ on line 294 $current_enzyme = "BssSI"; on line 295
} elsif(uc($opts{s}) eq $enzyme{BssSI}){ on line 312 $current_enzyme = "BssSI"; on line 313

The 'hybrid' function supports ‘BssSI’ if users use the latest BioNano scripts

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liufuyan2016 commented 4 years ago

Does the data labled by the DLE-1 enzyme from DLS platform could be use this pipeline for analysis?

yyx8671 commented 4 years ago

Have not tested DLE-1. Probably it works.