Hi,
Thank you for the excellent work you all do! I have run the commands and generated results, am currently in the analysing stage. While cross-checking with the pipeline steps, I came across some basic doubts about the input for build files which I would like to clarify.
Are there any specific parameters to be noted while STAR mapping (the recommended tool, right?) that is suitable for known and novel junction recognition by MAJIQ? Like any thresholds or parameters to be set that makes the bam files more suitable for efficient splice graph formation?
Also, is the
GENCODE .gff3 file okay? Or are there preferences for specific annotation files to be included? like from Ensembl or something?
Thank you!
Kind regards,
Swethaa