329ef2e1f93ff5e7c00ffdf3b5fe97e65a86a066 max Fri Jan 24 05:33:54 2020 -0800 improving RefSeq Select docs, refs #24787 diff --git src/hg/makeDb/trackDb/refSeqComposite.html src/hg/makeDb/trackDb/refSeqComposite.html index e6350fa..f00308c 100644 --- src/hg/makeDb/trackDb/refSeqComposite.html +++ src/hg/makeDb/trackDb/refSeqComposite.html @@ -38,39 +38,39 @@ <li> <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.</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 mentioned in the Human - Gene Mutation Database. This track is only available on the human genomes hg19 and hg38. + <em>RefSeq Select</em> – only show transcripts marked as <a href="https://www.ncbi.nlm.nih.gov/refseq/refseq_select/" target=_blank>RefSeq Select</a>. For each protein coding gene, there is a single "RefSeq Select" transcript. + Some of them are also in the <a href="https://www.ncbi.nlm.nih.gov/refseq/MANE/" target=_blank>MANE</a> track, these transcripts have a 100% match in the Ensembl/Gencode gene transcript annotation. This subset is only available on + the human genomes hg19 and hg38 at the moment. </li> <li> - <em>RefSeq Select</em> – only show transcript marked as <a href="https://www.ncbi.nlm.nih.gov/refseq/refseq_select/" target=_blank>RefSeq Select</a> or <a href="https://www.ncbi.nlm.nih.gov/refseq/MANE/" target=_blank>MANE</a>. - 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 RefSeq and Ensembl/GENCODE, and have a 100% - identical match to a transcript in the Ensembl annotation. </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> </ul> </dl> <dl> <dt><em><strong>UCSC annotations</strong></em></dt> <ul> <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> </ul> </dl> <p> The <em>RefSeq All</em>, <em>RefSeq Curated</em>, <em>RefSeq Predicted</em>, <em>RefSeq Clinical</em>