genome file

[naqvia]

I get the following error:

usage: __main__.py [-h] [-o OUT] [-r READ] [-m] [-c] [-q q_lo q_hi] [--g_or_ln G_OR_LN] rmats_folder gtf_file genome
__main__.py: error: unrecognized arguments: --splice_type /Users/naqvia/Downloads/hg38.fa

My command is:

python -m jcast -o test -r 10 --splice_type SE ~/project/22ad05b4-65d1-4269-b585-260c91403d7b.SE.MATS.JC.txt ~/data/gencode.v33.primary_assembly.annotation.gtf ~/data/hg38.fa

Do you know why? I have also tried just using -s, but I get the same issues.

[ed-lau]

Can you check the version of JCAST? The --splice_type flag is only in v.0.3.5a https://github.com/ed-lau/jcast/releases
Also I would check that you provide the path to the rMATS output folder rather than the specific JC.txt file.