Frequently Asked Questions

JCAST software for alternative splicing proteomics analysis. Create custom protein databases using RNA-seq data to identify unique protein alternative splicing isoforms in mass spectrometry experiments

Edward Lau, Maggie Lam


October 31, 2022

This page provides the documentation for the JCAST package, which is a tool for create a database of protein isoforms from RNA-seq data.


Q: What do I do with the output files?

A: For a typical application, we would recommend appending T1.fasta to either the JCAST canonical output (which writes the canonical sequence for any gene that has been detected above the read count cutoff, regardless of whether the non-canonical translation was successful), or to a Uniprot canonical database. The lower tier fasta files contain sequences with frame shifts and/or termination codons. You can include them by appending them to the T1+canonical fasta, but the results should be interpreted with caution.

Q: What files are required in the rMATS directory input?

A: JCAST expects a typical unaltered rMATS output folder, including the individual splice types from rMATS being in the rMATS output directory, named exactly as MXE.MATS.JC.txt, SE.MATS.JC.txt, RI.MATS.JC.txt, A3SS.MATS.JC.txt, A5SS.MATS.JC.txt.

Q: How can I contribute to JCAST?

A: Contact us at