Command Line Reference

sqanti3_to_UCSC.py

Main conversion tool for creating UCSC track hubs.

Required Arguments

Argument	Description
--gtf	Path to SQANTI3 corrected GTF file
--classification	Path to SQANTI3 classification file
--output	Output directory for generated files
--genome	Genome assembly name (e.g., hg38, mm10, dm6)

Optional Arguments

Argument	Default	Description
--chrom-sizes	-	Path to chromosome sizes file
--twobit	-	Path to genome .2bit file (alternative to chrom-sizes)
--github-repo	-	GitHub repository (format: username/repository) for raw URLs
--github-branch	main	GitHub branch
--star-sj	-	Path to STAR SJ.out.tab for splice junctions track
--tables	False	Generate interactive HTML tables for each category
--sort-by	iso_exp	Sort isoforms by metric (see below)
--no-category-tracks	False	Only generate the main track
--keep-temp	False	Keep temporary files for debugging
--validate-only	False	Validate inputs and exit
--dry-run	False	Process up to BED file, skip bigBed/hub

Sort-by Options

Option	Description	Order
iso_exp	Isoform expression	Highest first
length	Transcript length	Longest first
FL	Full-length reads	Highest first
diff_to_TSS	Distance to reference TSS	Closest first
diff_to_TTS	Distance to reference TTS	Closest first
diff_to_gene_TSS	Distance to gene TSS	Closest first
diff_to_gene_TTS	Distance to gene TTS	Closest first
dist_to_CAGE_peak	Distance to CAGE peak	Closest first
dist_to_polyA_site	Distance to polyA site	Closest first

---

filter_isoforms.py

Standalone tool for generating interactive HTML reports.

Required Arguments

Argument	Description
--classification	Path to SQANTI3 classification file
--output-dir	Output directory for HTML reports

Optional Arguments

Argument	Default	Description
--include-sequences	False	Include ORF_seq column (excluded by default)

---

Examples

Basic conversion:

python sqanti3_to_UCSC.py \
    --gtf corrected.gtf \
    --classification classification.txt \
    --output hub \
    --genome hg38

Full-featured conversion:

python sqanti3_to_UCSC.py \
    --gtf corrected.gtf \
    --classification classification.txt \
    --output hub \
    --genome hg38 \
    --github-repo user/repo \
    --tables \
    --sort-by iso_exp \
    --star-sj SJ.out.tab

Standalone HTML reports:

python filter_isoforms.py \
    --classification classification.txt \
    --output-dir reports