Additional Steps for Customised Gencode version for CTAT-Mutations

[Kent Fung]

Hi all,

I am trying to use CTAT-Mutations on some human RNA-Seq samples. Due to the need for using it on different project, I might need a difference GENCODE version for each of them. From what I understand I can use ctat-genome-lib-builder to build the ctat genome library from an available data source. However, I am just wondering if the CTAT Mutation Lib Supplement is compatible/independent of GENCODE version, as long as it is the same genome version (GRCh38 in my case).

And on a side note, is the STAR alignment run on CTAT Mutation compatible with STAR fusion in terms of settings (as suggested on STAR-Fusion wiki)? And does it save the bam files so I can have them for later use?

Thank you very much for your help!

Kent