Output Files

Directory Structure

output_directory/
├── hub.txt                              # Main hub configuration
├── genomes.txt                          # Genome assembly mapping
├── README.md                            # Hub documentation
├── {genome}_classification.txt          # Copy of classification file
├── {genome}_sqanti3.bb                  # Main bigBed with all transcripts
├── {genome}_sqanti3_full-splice_match.bb      # Category-specific bigBed
├── {genome}_sqanti3_incomplete-splice_match.bb
├── {genome}_sqanti3_novel_in_catalog.bb
├── {genome}_sqanti3_novel_not_in_catalog.bb
├── {genome}_sqanti3_genic.bb
├── {genome}_sqanti3_antisense.bb
├── {genome}_sqanti3_fusion.bb
├── {genome}_sqanti3_intergenic.bb
├── {genome}_sqanti3_genic_intron.bb
├── {genome}_sqanti3_track.html          # Main track documentation
├── {genome}_sqanti3_*.html              # Category track documentation
├── {output}_{genome}_SQANTI3_Hub.html   # Hub description page
├── {genome}/
│   ├── trackDb.txt                      # Track configuration
│   ├── groups.txt                       # Track groups
│   ├── trix.ix                          # Trix search index
│   └── trix.ixx                         # Trix search index
└── table_reports/                       # (if --tables flag used)
    ├── full-splice_match_isoforms.html
    ├── incomplete-splice_match_isoforms.html
    ├── novel_in_catalog_isoforms.html
    └── ...                              # One HTML per category

File Descriptions

Hub Configuration Files

File	Description
hub.txt	Main hub entry point - contains hub name, email, and references
genomes.txt	Maps genome assembly to trackDb location
trackDb.txt	Defines all tracks, filters, and display settings
groups.txt	Defines track groups for organization

BigBed Files

File	Description
{genome}_sqanti3.bb	All transcripts colored by structural category
{genome}_sqanti3_{category}.bb	Transcripts of a single category
{genome}_star_sj.bb	STAR splice junctions (if --star-sj used)

Trix Index Files

File	Description
trix.ix	Main search index
trix.ixx	Secondary index for efficient lookups

Documentation Files

File	Description
README.md	Hub usage instructions
{genome}_sqanti3_track.html	Filter documentation for main track
{genome}_sqanti3_{category}.html	Filter documentation for category tracks
{output}_{genome}_SQANTI3_Hub.html	Hub description page

HTML Reports (with --tables)

File	Description
{category}_isoforms.html	Interactive table with all columns, filters, and export

BigBed Format

The bigBed files use BED12+N format where N is the number of extra columns from the classification file.

Standard BED12 Columns

Column	Description
chrom	Chromosome
chromStart	Start position
chromEnd	End position
name	Isoform ID
score	Score (0-1000)
strand	+ or -
thickStart	CDS start
thickEnd	CDS end
itemRgb	Color (RGB)
blockCount	Number of exons
blockSizes	Exon sizes
chromStarts	Exon starts

Extra Columns

All columns from the classification file are included, such as:

• structural_category
• associated_gene
• associated_transcript
• coding
• iso_exp
• FL
• And many more...