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kvittingseerup / IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
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CPAT3 compatibility #235

Open rugilemat opened 3 months ago

rugilemat commented 3 months ago

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!

chunxubioinfor commented 2 months ago

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.

rugilemat commented 2 months ago

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