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gagneurlab / FRASER

FRASER - Find RAre Splicing Events in RNA-seq
MIT License
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Adapt the script for mouse? #84

Closed fburdet closed 3 months ago

fburdet commented 1 year ago

Hello,

First of all, is this code still maintained? I received absolutely no news despite writing directly to the author.

My question is, is it possible to adapt the code for mouse data?

I tried to use library(TxDb.Mmusculus.UCSC.mm10.knownGene) library(org.Mm.eg.db)

but I get errors about chromosome length, I suspect it's hardcoded to use human, is it the case?

It makes most of the plotting functions not usable, as they seem to depend on this annotation.

cayyya commented 1 year ago

I have similar problem but with Arabidopsis and I cant even reach the plotting stage. fds <- countRNAData(settings) yields following error: Error in .replace_seqlevels_style(x_seqlevels, value) : found no sequence renaming map compatible with seqname style "TAIR9" for this object

Is there any hint how to set up the workflow for Arabidopsis?

vyepez88 commented 3 months ago

Hi, sorry for the late reply. Yes, at this stage, we only support human.