command_line_reference

Command Line Reference

Complete reference for all command-line options.

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sqanti_browser.py

Main tool for converting SQANTI3 outputs to UCSC track hubs.

How to run: Use python -m sqanti_browser (recommended), or sqanti_browser after pip install -e ., or python sqanti_browser.py from project root. See Installation for details.

Required Arguments

Argument	Description
--gtf	SQANTI3 corrected GTF file
--classification	SQANTI3 classification file
--output	Output directory for hub files
--genome	Genome assembly (hg38, mm10, or custom name with --twobit)

Common Optional Arguments

Argument	Default	Description
--tables	False	Generate interactive HTML reports (recommended)
--sort-by	basic	Sort isoforms. basic (default), none (preserve GTF order), or metric (see options)
--no-category-tracks	False	Skip individual category tracks (faster)
--category-tracks	All	Only create tracks for listed categories. Comma-separated abbreviated names: FSM, ISM, NIC, NNC, antisense, genic_intron, genic_genomic (or genic), intergenic, fusion. Example: --category-tracks FSM,ISM,NIC
--hub-name	(none)	Display name for this hub and prefix for all track labels. Use when loading multiple hubs to compare (e.g. SQANTI-reads samples). Tracks appear as "Name SQANTI3 Transcripts", "Name full-splice_match", etc.
--trix	True	Explicitly enable Trix index generation (default behavior; requires ixIxx in PATH)
--no-trix	False	Disable Trix index generation (skip creating trix.ix/trix.ixx)

Genome Options

Argument	Description
--chrom-sizes	Chromosome sizes file (auto-detected for standard genomes)
--twobit	.2bit file for custom genomes (auto-extracts chrom sizes)

Tip: Use --twobit for non-model organisms. See Custom Genomes.

Validation Tracks

Add optional tracks to assess transcript quality:

Argument	What It Validates	When to Use
--refGTF	Shows reference annotation	Always recommended!
--star-sj	Short-read junction support	You have STAR output
--CAGE-peak	Transcription start sites (5' ends)	Assess TSS accuracy
--polyA-peak	Termination sites (3' ends)	Assess TTS accuracy

Where to get these files:

• refGTF: Same file used with SQANTI3 (GENCODE, Ensembl)
• CAGE/polyA: See SQANTI3 CAGE docs and polyA docs

Debugging Options

Argument	What It Does
--validate-only	Check inputs without creating hub (fast)
--dry-run	Process data but skip bigBed creation
--keep-temp	Keep temporary files for inspection
--no-highlight	Disable highlight coloring for top FL isoforms

Sorting Options

Control how isoforms are ordered within each genomic position:

Option	Sorts By	Order
none	No sorting (default)	Arbitrary
FL	Full-length read count	Most first
iso_exp	Short read expression for this isoform	Highest first
length	Transcript length	Longest first
diff_to_TSS	Distance to reference TSS	Closest first
diff_to_TTS	Distance to reference TTS	Closest first
dist_to_CAGE_peak	Distance to CAGE peak	Closest first
dist_to_polyA_site	Distance to polyA site	Closest first

Note: Sorting affects display order in UCSC but does NOT filter data. See Isoform Ordering.

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src/filter_isoforms.py

Generate standalone HTML reports without creating a track hub. Run from the project root.

Arguments

Argument	Required	Default	Description
--classification	Yes	-	SQANTI3 classification file
--output-dir	Yes	-	Output directory for reports
--include-sequences	No	False	Include ORF_seq column

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Quick Examples

Minimal Command

python -m sqanti_browser \
    --gtf corrected.gtf \
    --classification classification.txt \
    --output my_hub \
    --genome hg38

Recommended (With Tables)

python -m sqanti_browser \
    --gtf corrected.gtf \
    --classification classification.txt \
    --output my_hub \
    --genome hg38 \
    --tables

Full Validation Tracks

python -m sqanti_browser \
    --gtf corrected.gtf \
    --classification classification.txt \
    --output my_hub \
    --genome hg38 \
    --refGTF reference.gtf \
    --star-sj SJ.out.tab \
    --CAGE-peak CAGE_peaks.bed \
    --polyA-peak polyA_peaks.bed \
    --tables \
    --sort-by iso_exp

Custom Genome

python -m sqanti_browser \
    --gtf corrected.gtf \
    --classification classification.txt \
    --output my_hub \
    --genome my_species_v1 \
    --twobit genome.2bit \
    --tables

Standalone HTML Reports

python src/filter_isoforms.py \
    --classification classification.txt \
    --output-dir reports \
    --include-sequences

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See Also

• Quick Reference - One-page cheat sheet
• Usage Examples - More examples with explanations
• Custom Genomes - Working with .2bit files
• Isoform Ordering - How sorting works

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