df8c8dcd64bc7d71f9711df629b6d0178d6fa26f max Tue Feb 25 13:33:12 2020 -0800 trying to reduce the confusion in docs between refseq select and MANE, refs #24787 diff --git src/hg/makeDb/trackDb/refSeqComposite.html src/hg/makeDb/trackDb/refSeqComposite.html index 1e0002c..400e476 100644 --- src/hg/makeDb/trackDb/refSeqComposite.html +++ src/hg/makeDb/trackDb/refSeqComposite.html @@ -38,51 +38,53 @@ <em>RefSeq Predicted</em> – subset of RefSeq All that includes those annotations whose accessions begin with XM or XR.</li> <li> <em>RefSeq Other</em> – all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the <em>RefSeq Curated</em> or the <em>RefSeq Predicted</em> tracks.</li> <li> <em>RefSeq Alignments</em> – alignments of RefSeq RNAs to the $organism genome provided by the RefSeq group, following the display conventions for <a href="../goldenPath/help/hgTracksHelp.html#PSLDisplay" target="_blank">PSL tracks</a>.</li> <li> <em>RefSeq Diffs</em> – alignment differences between the $organism reference genome(s) and RefSeq transcripts. <small>(Track not currently available for every assembly.)</small> </li> <li> - <em>RefSeq HGMD</em> – only show RefSeq Curated transcripts annotated by the Human - Gene Mutation Database. This track is only available on the human genomes hg19 and hg38. - It is the most restricted RefSeq subset, targeting clinical diagnostics. - </li> + <em>UCSC RefSeq</em> – annotations generated from UCSC's realignment of RNAs with NM + and NR accessions to the $organism genome. This track was previously known as the "RefSeq + Genes" track.</li> <li> - <em>RefSeq Select/MANE</em> – only show transcript marked as RefSeq Select or MANE Select. + <em>RefSeq Select+MANE (subset)</em> – Subset of RefSeq Curated, transcripts marked as RefSeq Select or MANE Select. A single Select transcript is chosen as representative for each protein-coding gene. - Transcripts categorized as MANE are further agreed upon as representative by both NCBI + This track includes transcripts categorized as MANE, they are further agreed upon as representative by both NCBI RefSeq and Ensembl/GENCODE, and have a 100% identical match to a transcript in the Ensembl annotation. See <a target="_blank" href="https://www.ncbi.nlm.nih.gov/refseq/refseq_select/">NCBI RefSeq Select</a>. + Note that we provide a separate track <a target=_blank href="hgTrackUi?g=mane">MANE</a>, + which contains only the MANE transcripts, and not the ones specific to RefSeq. </li> <li> - <em>UCSC RefSeq</em> – annotations generated from UCSC's realignment of RNAs with NM - and NR accessions to the $organism genome. This track was previously known as the "RefSeq - Genes" track.</li> + <em>RefSeq HGMD (subset)</em> – Subset of RefSeq Curated, transcripts annotated by the Human + Gene Mutation Database. This track is only available on the human genomes hg19 and hg38. + It is the most restricted RefSeq subset, targeting clinical diagnostics. + </li> </ul> </dl> <p> -The <em>RefSeq All</em>, <em>RefSeq Curated</em>, <em>RefSeq Predicted</em>, <em>RefSeq Clinical</em>, +The <em>RefSeq All</em>, <em>RefSeq Curated</em>, <em>RefSeq Predicted</em>, <em>RefSeq HGMD</em>, <em>RefSeq Select/MANE</em> and <em>UCSC RefSeq</em> tracks follow the display conventions for <a href="../goldenPath/help/hgTracksHelp.html#GeneDisplay" target="_blank">gene prediction tracks</a>. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), or reviewed (dark), as defined by <a target=_blank href="https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_status_codes/?report=objectonly">RefSeq</a>. </p> <p> <table> <thead> <tr> <th style="border-bottom: 2px solid #6678B1;">Color</th> <th style="border-bottom: 2px solid #6678B1;">Level of review</th> </tr> </thead> <tr>