c71281301ba035188bb402d91d6940aad6b0c12a gperez2 Mon May 2 15:21:44 2022 -0700 Updating the html for the non-human ncbiRefSeq tracks, refs #29127 diff --git src/hg/makeDb/trackDb/refSeqComposite.html src/hg/makeDb/trackDb/refSeqComposite.html index bd71253..80b8859 100644 --- src/hg/makeDb/trackDb/refSeqComposite.html +++ src/hg/makeDb/trackDb/refSeqComposite.html @@ -42,53 +42,34 @@ <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>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 (subset)</em> – Subset of RefSeq Curated, transcripts marked as - RefSeq Select or MANE Select. - A single <em>Select</em> transcript is chosen as representative for each protein-coding gene. - This track includes transcripts categorized as MANE, which 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&db=hg38&c=chr22">MANE (hg38)</a>, - which contains only the MANE transcripts. - </li> - <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 HGMD</em>, -<em>RefSeq Select/MANE</em> and <em>UCSC RefSeq</em> tracks follow the display conventions for +The <em>RefSeq All</em>, <em>RefSeq Curated</em>, <em>RefSeq Predicted</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> <th bgcolor="#0C0C78"></th> @@ -197,32 +178,30 @@ in the <a href="https://hgdownload.soe.ucsc.edu/goldenPath/archive/$db/ncbiRefSeq/" target="_blank">archives</a> of our downloads server. You can also access any RefSeq table entries in JSON format through our <a href="http://genome.ucsc.edu/goldenPath/help/api.html"> JSON API</a>.</p> <p> The data in the <em>RefSeq Other</em> and <em>RefSeq Diffs</em> tracks are organized in <a href="../../FAQ/FAQformat.html#format1.5" target="_blank">bigBed</a> file format; more information about accessing the information in this bigBed file can be found below. The other subtracks are associated with database tables as follows:</p> <dl> <dt><a href="../../FAQ/FAQformat.html#format9" target="_blank">genePred</a> format:</dt> <ul> <li>RefSeq All - <tt>ncbiRefSeq</tt></li> <li>RefSeq Curated - <tt>ncbiRefSeqCurated</tt></li> <li>RefSeq Predicted - <tt>ncbiRefSeqPredicted</tt></li> - <li>RefSeq HGMD - <tt>ncbiRefSeqHgmd</tt></li> - <li>RefSeq Select+MANE - <tt>ncbiRefSeqSelect</tt></li> <li>UCSC RefSeq - <tt>refGene</tt></li> </ul> <dt><a href="../../FAQ/FAQformat.html#format2" target="_blank">PSL</a> format:</dt> <ul> <li>RefSeq Alignments - <tt>ncbiRefSeqPsl</tt></li> </ul> </dl> <p> The first column of each of these tables is "bin". This column is designed to speed up access for display in the Genome Browser, but can be safely ignored in downstream analysis. You can read more about the bin indexing system <a href="http://genomewiki.ucsc.edu/index.php/Bin_indexing_system" target="_blank">here</a>.</p> <p> The annotations in the <em>RefSeqOther</em> and <em>RefSeqDiffs</em> tracks are stored in bigBed files, which can be obtained from our downloads server here,