Trix Search

The tool generates a Trix search index that enables powerful text-based search in the UCSC Genome Browser search box.

Basic Search

Search Term	Description	Example
`isoform_id`	Search by exact isoform ID	`PB.1234.1`
`gene_name`	Search by associated gene	`BRCA1` or `ENSG00000012048`

Use prefixed terms to filter by specific attributes:

Search Term	Description	Example
`structural_category_X`	Filter by structural category	`structural_category_novel_in_catalog`
`strand_plus` / `strand_minus`	Filter by strand	`strand_plus`
`coding_coding` / `coding_non_coding`	Filter by coding status	`coding_coding`
`subcategory_X`	Filter by subcategory	`subcategory_mono-exon`
`bite_True` / `bite_False`	Filter by BITE status	`bite_True`
`predicted_NMD_True`	Filter by NMD prediction	`predicted_NMD_True`
`polyA_motif_found_True`	Filter by polyA motif	`polyA_motif_found_True`
`RTS_stage_True`	Filter by RTS stage	`RTS_stage_True`
`within_CAGE_peak_True`	Filter by CAGE peak	`within_CAGE_peak_True`

Combine multiple terms with spaces (AND logic):

structural_category_novel_in_catalog strand_plus coding_coding

This finds all novel_in_catalog isoforms on the plus strand that are coding.

BRCA1 structural_category_full-splice_match

structural_category_novel_in_catalog strand_minus coding_coding

predicted_NMD_True

subcategory_mono-exon

The HTML reports include a "Generate Trix String" button:

Filter-based: Set your desired filters using dropdowns, then click "Generate Trix String"
Row-based: Click on a specific isoform row to select it (highlighted in blue), then click "Generate Trix String"

The generated string can be copied directly into the UCSC Genome Browser search box.

Note: Range filters (e.g., 100:1000 for length) are not supported by Trix search and will be ignored.