d328b0a2a09c271ddaee177d6405fac096371dc4 lrnassar Thu Jul 4 09:17:53 2019 -0700 Updating FAQ on how we generate knownCanonical for hg38 #23748 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 92f6ed4..2c741e3 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -370,55 +370,58 @@ alt="Changing splice variants" width="750"> <p>For the track <a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite"> NCBI RefSeq</a> (hg38), you can activate the subtrack "RefSeq HGMD". It contains only the transcripts that are part of the Human Gene Mutation Database. </p> <a name="singledownload"></a> <h6>How can I download a file with a single transcript per gene?</h6> <p> This is a common request, but very often this is not necessary when designing an analysis. You will have to make a choice of this single transcript using some mechanism, and this choice will affect your pipeline results. It may be easier to keep all transcripts. For example, instead of annotating enhancers -with the closest "best-transcript", you can annotate them with the closest exon +with the closest "best-transcript", you can annotate them with the closest exon of any transcript. When mapping variants to transcripts, you can map to all transcripts and sort these by accession ID, showing mainly the first. When segmenting the chromosomes into gene loci, you can use the union of all transcripts of a gene rather than select a single "best" transcript. </p> <p> -That being said, data tables called "knownCanonical" are available for +That being said, data tables called "knownCanonical" are available for many assemblies. They try to select only a single transcript/isoform per gene, if possible.</p> <p> For hg19, the knownCanonical table is a subset of the <a target="_blank" href="../cgi-bin/hgTrackUi?db=hg19&g=knownGene">UCSC Genes</a> track. It was generated by identifying a canonical isoform for each cluster ID, or gene. Generally, this is the longest isoform. It can be downloaded directly from the <a target="_blank" href="http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/">hg19 downloads database</a> or by using the <a target="_blank" href="../cgi-bin/hgTables">Table Browser</a>.</p> <p> For hg38, the knownCanonical table is a subset of the <a target="_blank" href="../cgi-bin/hgTrackUi?db=hg38&g=knownGene">GENCODE v29</a> track. As opposed to the hg19 -equivalent which generally used the longest isoform for indentification, this table is defined -as follows:</p> +knownCanonical table, which used computationally generated gene clusters and generally chose the +longest isoform as the canonical isoform, the hg38 table uses ENSEMBL gene IDs to define clusters +(that is to say, one canonical isoform per ENSEMBL gene ID), and the method of choosing the +isoform is described as such:</p> + <p> <i>knownCanonical identifies the canonical isoform of each cluster ID or gene using the ENSEMBL gene IDs to define each cluster. The canonical transcript is chosen using the APPRIS principal transcript when available. If no APPRIS tag exists for any transcript associated with the cluster, then a transcript in the BASIC set is chosen. If no BASIC transcript exists, then the longest isoform is used.</i></p> <p> It can be downloaded directly from the <a target="_blank" href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/">hg38 downloads database</a> or by using the <a target="_blank" href="../cgi-bin/hgTables">Table Browser</a>.</p> <a name="whatdo"></a> <h6>This is rather complicated. Can you tell me which gene transcript track I should use?</h6> <p> For automated analysis, if you are doing NGS analysis and you need to capture