I'm trying to generate a index for HISAT2 but am facing trouble extracting exons and splice sites.
When I try to do so, these are the errors I get:
/usr/bin/shifter: hisat2_extract_splice_sites.py: No such file or directory
/usr/bin/shifter: hisat2_extract_exons.py: No such file or directory
I'm using HISAT2 from a docker image so I thought maybe it is not finding the path to the tool? Although the command hisat2-build runs fine, and I am able to generate the index without these options with no problem.
I'm new to bioinformatics so I'm sorry if my question is too basic. Thanks a lot