e863249eae18325e041c2948722b98cb5a5643e4
markd
  Fri Nov 4 14:47:29 2022 -0700
Dropped GENCODE 2-way pseudogenes from latest releases.  These should have never been included

diff --git src/hg/makeDb/trackDb/wgEncodeGencodeDisplay1.shared.html src/hg/makeDb/trackDb/wgEncodeGencodeDisplay1.shared.html
index 7cf2a6a..e86dba6 100644
--- src/hg/makeDb/trackDb/wgEncodeGencodeDisplay1.shared.html
+++ src/hg/makeDb/trackDb/wgEncodeGencodeDisplay1.shared.html
@@ -8,46 +8,30 @@
 <b>Views</b> available on this track are:
 <dl>
     <dt><i>Genes</i></dt>
     <dd> The gene annotations in this view are divided into three subtracks:</dd>
 </dl>
 <ul>
   <li><em>GENCODE Basic set</em> is a subset of the <em>Comprehensive set</em>. 
     The selection criteria are described in the <a href="#basicSetSelection">methods section</a>.</li>
   <li><em>GENCODE Comprehensive set</em> contains all GENCODE coding and non-coding transcript annotations,
     including polymorphic pseudogenes.  This includes both manual and
     automatic annotations.  This is a super-set of the <em>Basic set</em>.</li>
   <li><em>GENCODE Pseudogenes</em> include all annotations except polymorphic pseudogenes.</li>
 </ul>
     
 <dl>
-    <dt><i>2-way</i></dt> 
-</dl>
-<ul>
-    <li><em>GENCODE 2-way Pseudogenes</em> contains pseudogenes predicted by both the 
-        <a href="https://academic.oup.com/bioinformatics/article-abstract/22/12/1437/207326">Yale
-        PseudoPipe</a> and
-        <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-466">
-        UCSC RetroFinder</a> pipelines. The set was derived by looking for 50 base pairs
-        of overlap between pseudogenes derived from both sets based on their 
-        chromosomal coordinates.  When multiple PseudoPipe
-        predictions map to a single RetroFinder prediction, only one match is kept
-        for the 2-way consensus set.
-    </li>
-</ul>
-
-<dl>
     <dt><i>PolyA</i></dt>
 </dl>
 <ul>
 <li><em>GENCODE PolyA</em> contains polyA signals and sites manually annotated on
     the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of
     transcripts containing at least 3 A's not matching the genome.</li>
 </ul>
 
 <p>
 <b>Maximum number of transcripts to display</b>
 is available for the items in the GENCODE Basic, Comprehensive and Pseudogene tracks.
 Starting with the GENCODE human V42 and mouse VM31 releases, 
 transcripts are assigned rank within the gene. The ranks may be used to filter the number of transcripts
 displayed in a principled manner.  Transcript ranking is not available in the <em>lift37</em> releases.
 See <a href="#Methods">Methods</a> for details of rank assignment.
@@ -79,31 +63,30 @@
      <li> automatic_only - display automatically created annotations that were
        not annotated by the manual method</li>
    </ul>
    </li>
   <li> Transcript Biotype: filter transcripts by
        <a href="https://www.gencodegenes.org/pages/biotypes.html" target="_blank">Biotype</a></li>
   <li> Support Level: filter transcripts by <a href="#tsl">transcription support level</a></li>
 </ul>
 
 <p><b>Coloring</b> for the gene annotations is based on the annotation type: </p>
 <ul>
   <li><font color="#0c0c78"><b>coding</b></font> 
   <li><font color="#006400"><b>non-coding</b></font> 
   <li><font color="#ff33ff"><b>pseudogene</b></font> 
   <li><font color="#fe0000"><b>problem</b></font>
-  <li><font color="#ff33ff"><b>all 2-way pseudogenes</b></font>
   <li><font color="#000000"><b>all polyA annotations</b></font>
 </ul>
 
 <h2 id="Methods">Methods</h2>
 
 <p>
 The GENCODE project aims to annotate all evidence-based gene features on the 
 human and mouse reference sequence with high accuracy by integrating 
 computational approaches (including comparative methods), manual
 annotation and targeted experimental verification. This goal includes identifying 
 all protein-coding loci with associated alternative variants, non-coding
 loci which have transcript evidence, and pseudogenes. 
 For a detailed description of the methods and references used, see
 Harrow <em>et al.</em> (2006).
 </p>