Is Arabidopsis thaliana available for msPIPE (species that do not have UCSC version name)?

[ZhujunYao]

Arabidopsis thaliana's genome does not have a specific UCSC version name; instead, it is imported into UCSC from the TAIR website. Arabidopsis is a widely recognized model organism for biological research. Is there a way to make msPIPE available for BS-seq analysis for Arabidopsis?

[heesun9]

Since msPIPE obtains UCSC data via BS genome Rpackage, analysis can be difficult for species without that data.
However, if you manually provide the downloaded reference files (fasta,gtf) to the pipeline, basic methylation calling analyses are possible.