I’m trying to extract features from a GTF file using hisat2. This is the code that I am using:
cd $RNA_REFS_DIR hisat2_extract_splice_sites.py $RNA_REF_GTF > $RNA_REFS_DIR/splicesites.tsv hisat2_extract_exons.py $RNA_REF_GTF > $RNA_REFS_DIR/exons.tsv hisat2-build -p 8 --ss $RNA_REFS_DIR/splicesites.tsv --exon $RNA_REFS_DIR/exons.tsv $RNA_REF_FASTA $RNA_REF_INDEX
but I keep getting errors that none of the commands are found.
hisat2_extract_splice_sites.py :command not found
-bash extract_exons.py :command not found
-bash build.py :command not found
I’m not sure if this is an issue with hisat2 or with compute canada.
Any help would be really appreciated!