Hisat2 Extract Splice Sites Py

# Extract splice junctions from a GTF file
hisat2_extract_splice_sites.py annotation.gtf > splicesites.txt

# Print progress/statistics to stderr
hisat2_extract_splice_sites.py -v annotation.gtf > splicesites.txt

# Stream a compressed GTF via stdin
gzip -cd annotation.gtf.gz | hisat2_extract_splice_sites.py - > splicesites.txt

# Reuse the result during HISAT2 index building
hisat2-build-s genome.fa genome --ss splicesites.txt

Recommended Workflow

1. Obtain a valid GTF annotation file for your reference organism
2. Run hisat2_extract_splice_sites.py annotation.gtf > splice_sites.txt
3. Pass the output file to HISAT2 index building via --ss option
4. Add -v flag if you want diagnostic statistics printed to stderr

Guardrails

• Input must be a valid GTF file or "-" to read from stdin
• Output writes to stdout; redirect to a file to save results
• Use -v only when you want progress/statistics reported to stderr
• This helper does not implement --version; use -h/--help for availability checks