9f6962c173c405e481da17794d67107e7f8e73a9 jnavarr5 Fri Oct 2 16:05:31 2026 -0700 Replacing the subtrack matrix and Sample class filter paragraph on the PRO-cap and ProCapNet description pages with the track collection layout from Mark's change, and noting that ProCapNet minus strand files store negative values, refs #35528 diff --git src/hg/makeDb/trackDb/human/proCapNet.html src/hg/makeDb/trackDb/human/proCapNet.html index 463d03e2645..e904555336b 100644 --- src/hg/makeDb/trackDb/human/proCapNet.html +++ src/hg/makeDb/trackDb/human/proCapNet.html @@ -31,34 +31,35 @@ <p> The predictions are available on GRCh38/hg38 and T2T-CHM13/hs1. The contribution scores are available on GRCh38/hg38 only, because they are computed at MANE Select transcription start sites and MANE is not defined for T2T-CHM13. </p> <p> Predictions are not measurements: they say what the sequence looks capable of, not what a given cell is doing. The matching experimental data is in the PRO-cap track, available on GRCh38/hg38. </p> <h2>Display Conventions and Configuration</h2> <p> -The matrix on this page has one row per cell line and one column per data type, -so a checkbox turns on one strand of one cell line's predictions, or its -contribution scores. Use the <b>Sample class</b> filter to restrict the matrix to -cancer or non-cancer lines. +This track collection holds one predicted PRO-cap track per cell line, shown by +default, and on GRCh38/hg38 one contribution score track per cell line, hidden by +default. Use the buttons on this page to turn tracks on or off, and click a track's +name to open its own settings, where the plus and minus strands of a predicted +PRO-cap track can also be turned on separately. </p> <p> Each predicted PRO-cap track is an overlay of the two strands: plus strand predictions are drawn upward and minus strand predictions downward. The y axis is the predicted number of PRO-cap reads at that base. </p> <p> Contribution scores are drawn as a sequence logo when zoomed in far enough to show individual bases: the letter of the reference base is scaled by its score, so a run of tall letters is a motif the model relied on. At lower zoom the same values are drawn as a wiggle. Scores can be negative, meaning the base argued against initiation being placed where it was. Scores exist only in the roughly 2 kb window around each MANE Select transcription start site, about 38.7 Mb of @@ -126,31 +127,32 @@ <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/$db/transcriptionStart.txt" target="_blank">doc/$db/transcriptionStart.txt</a>, the scripts they run are in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/outside/proCapNet" target="_blank">makeDb/outside/proCapNet</a>, and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/$db/transcriptionStart.ra" target="_blank">trackDb/human/$db/transcriptionStart.ra</a>. </p> <h2>Data Access</h2> <p> The bigWig files are on our <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/proCapNet/" target="_blank">download server</a>. Predictions are under <tt>pred/</tt> and are named for the cell line, the model and the strand, for example <tt>K562.proCapNet.pos.bw</tt> and -<tt>K562.proCapNet.neg.bw</tt>. Contribution scores, which exist for GRCh38 only, +<tt>K562.proCapNet.neg.bw</tt>. Minus strand values are stored as negative +numbers. Contribution scores, which exist for GRCh38 only, are under <tt>contrib/</tt>, for example <tt>K562.proCapNet-contrib.bw</tt>. </p> <p> The data can be explored interactively in table format with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our <a href="https://api.genome.ucsc.edu" target="_blank">API</a>. The API returns one bigWig at a time, so name a single strand of one cell line rather than the container, for example track=<i>proCapNet_K562_pred_pos</i>. </p> <p> Individual regions or the whole genome annotation can be obtained using our tool