401476f97d2e31e0880a181adffea05aad28996c lrnassar Tue Feb 18 16:16:06 2020 -0800 Clarifying name of RefSeq Select/MANE and expanding track description page refs #24787 diff --git src/hg/makeDb/trackDb/refSeqComposite.html src/hg/makeDb/trackDb/refSeqComposite.html index abc53a0..1e0002c 100644 --- src/hg/makeDb/trackDb/refSeqComposite.html +++ src/hg/makeDb/trackDb/refSeqComposite.html @@ -8,31 +8,31 @@ <a href="#methods">Methods</a> section for more details about how the different tracks were created. </p> <p> Please visit NCBI's <a href="https://www.ncbi.nlm.nih.gov/projects/RefSeq/update.cgi" target="_blank">Feedback for Gene and Reference Sequences (RefSeq)</a> page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. </p> <p> For more information on the different gene tracks, see our <a target=_blank href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p> <h2>Display Conventions and Configuration</h2> <p> This track is a composite track that contains differing data sets. To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to -hide. </p> +hide. <b>Note:</b> Not all subtracts are available on all assemblies. </p> The subtracks available for this track include: <dl> <dt><em><strong>RefSeq aligned annotations and UCSC alignment of RefSeq annotations </strong></em></dt> <ul> <li> <em>RefSeq All</em> – all curated and predicted annotations provided by RefSeq.</li> <li> <em>RefSeq Curated</em> – subset of <em>RefSeq All</em> that includes only those annotations whose accessions begin with NM, NR, NP or YP. <small>(NP and YP are used only for protein-coding genes on the mitochondrion; YP is used for human only.)</small></li> <li> <em>RefSeq Predicted</em> – subset of RefSeq All that includes those annotations whose @@ -43,39 +43,47 @@ <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> <li> + <em>RefSeq Select/MANE</em> – only show transcript 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 + 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>. + </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> </ul> </dl> <p> -The <em>RefSeq All</em>, <em>RefSeq Curated</em>, <em>RefSeq Predicted</em>, <em>RefSeq Clinical</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>, <em>RefSeq Clinical</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> <th bgcolor="#0C0C78"></th> @@ -182,30 +190,31 @@ target="_blank">downloads server</a> for local processing. 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,