65e058417a3426cf2ee0100b1e47e3397c19fee3 gperez2 Thu Feb 26 16:51:18 2026 -0800 Adding a note about the Table Browser not allowing Genome as a query region for the JASPAR track, refs #37168 diff --git src/hg/makeDb/trackDb/jaspar.html src/hg/makeDb/trackDb/jaspar.html index 0394fe321c6..bbb48f2509e 100644 --- src/hg/makeDb/trackDb/jaspar.html +++ src/hg/makeDb/trackDb/jaspar.html @@ -147,32 +147,33 @@ <p> JASPAR 2018 used the TFBS Perl module (Lenhard and Wasserman 2002) and FIMO (Grant, Bailey, and Noble 2011), as distributed within the MEME suite (version 4.11.2) (Bailey <em>et al.</em> 2009). For scanning genomes with the BioPerl TFBS module, profiles were converted to PWMs and matches were kept with a relative score ≥ 0.8. For the FIMO scan, profiles were reformatted to MEME motifs and matches with a p-value < 0.05 were kept. TFBS predictions that were not consistent between the two methods (TFBS Perl module and FIMO) were removed. The remaining TFBS predictions were colored according to their FIMO p-value to allow for comparison of prediction confidence between different profiles.</p> <h2>Data Access</h2> <p> -JASPAR Transcription Factor Binding data includes billions of items. Limited regions can -be explored interactively with the +JASPAR Transcription Factor Binding data includes billions of items. +Because of the data size, the Table Browser does not allow "Genome" as a query region for this +track. Limited regions can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> and cross-referenced with <a href="../cgi-bin/hgIntegrator">Data Integrator</a>, although positional queries that are too big can lead to timing out. This results in a black page or truncated output. In this case, you may try reducing the chromosomal query to a smaller window.</p> <p> For programmatic access, the track can be accessed using the Genome Browser's <a href="../../goldenPath/help/api.html">REST API</a>. JASPAR annotations can be downloaded from the <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/jaspar">Genome Browser's download server</a> as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large.</p> <p> The utilities for working with bigBed-formatted binary files can be downloaded