22039ac84d886676950d2726f1c8ff2e57f890a4 markd Wed Feb 4 20:53:31 2026 -0800 update recount3 color coding descrption to make it a more obvious diff --git src/hg/makeDb/trackDb/recount3.html src/hg/makeDb/trackDb/recount3.html index 028a24b1cb4..f9afe383e5b 100644 --- src/hg/makeDb/trackDb/recount3.html +++ src/hg/makeDb/trackDb/recount3.html @@ -21,31 +21,31 @@ </p> <h2>Display Conventions</h2> <p> Intron items are colored based on splice junction motifs and read support. Darker colors indicate higher read coverage. Split read counts and splice motifs are shown on mouseover. By default, only introns with a minimum read count of 10,000 are shown. This threshold can be changed on the track configuration page. </p> <p> The intron items are color-coded (darker colors indicate higher coverage): </p> <ul> <li><b><font color="#00bfff">Sky blue</font></b>: GT donors and AG acceptors (CT and AC on the minus strand)</li> - <li><b><font color="#00ced1">Turquoise</font></b>: GC donors (GC on the minus strand)</li> + <li><b><font color="#00ced1">Turquoise</font></b>: GC donors and AG acceptors (CT and GC on the minus strand)</li> <li><b><font color="#ff8c00">Orange</font></b>: AT donors and AC acceptors (GT and AT on the minus strand)</li> <li><b><font color="#a9a9a9">Grey</font></b>: Non-canonical junction motifs. These could be sequencing errors, polymorphisms, or very rare U12 introns.</li> </ul> <p> Introns can be filtered by: </p> <ul> <li><b>Intron size</b> - Length of the intron. The default range is 30 to 100,000 bases.</li> <li><b>Split read count</b> - Number of split reads supporting the intron. The default is a minimum of 10,000 reads.</li> <li><b>Splice junction motif</b> - The motif is specified in the form <em>GT/AG</em>, with canonical motifs in uppercase and unknown motifs in lowercase.