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Published 20 hours ago • verified publisher icon kvittingseerup

CPAT3 compatibility

Open rugilemat opened this issue 10 months ago • 2 comments

Hi there,

As far as I understand it's not possible to use CPAT3 with IsoformSwitchAnalyzeR? Are there plans to include this compatibility? I'm struggling to make CPAT2 work and the web version only offers GRCh37 assembly while all my analyses are done with GRCh38.

Thanks!

rugilemat avatar Apr 05 '24 22:04 rugilemat

Hi @rugilemat, the update to support CPAT3 is on our schedule, and I think I will take a look this week. For now, I guess there are two solutions for you.

  1. You could run CPAT 2 locally and then it's possible to apply make_hexamer_tab.py and make_logitModel.py to generate a model with GRCh38.
  2. CPC2 is also a good alternative which provides hg38 option.

I will let you know if I finish the update.

chunxubioinfor avatar Apr 11 '24 08:04 chunxubioinfor

Thanks! I went down CPC2 route as I could get a local CPAT2 version to run. Looking forward to the update though!

rugilemat avatar Apr 13 '24 00:04 rugilemat