ConesaLab

Use whenever the user is working with SQANTI-browser — turning SQANTI3 QC output (a corrected GTF + classification file) into a UCSC Genome Browser track hub for visualizing and curating long-read transcriptomes. Covers the `sqanti_browser` command and all its flags, required/optional inputs, the track-hub output (hub.txt, genomes.txt, trackDb, bigBed, groups, trix search index, per-category and validation tracks), interactive HTML tables (`--tables`), hosting the hub and validating with hubCheck, UCSC filtering and Trix search, isoform ordering (`--sort-by`), custom color palettes (`--my-palette`), non-reference genomes (`--twobit`), curated subset sessions via the Table Browser, and SQANTI-reads multi-sample workflows. Trigger for any mention of SQANTI-browser, "SQANTI3 to UCSC", building a track hub / trackDb / bigBed from SQANTI3, or visualizing classified isoforms in the UCSC browser.