4137de18d409a3913bbbecfe5e1ab6f52a9715d1 max Fri Jul 2 06:42:43 2021 -0700 fixing small docs typo diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 8dd1306..9ed54e4 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -481,31 +481,31 @@ <a name="singledownload"></a> <h2>How can I download a file with a single transcript per gene?</h2> <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 of any transcript. When mapping variants to transcripts, you can map to all transcripts and and show the transcript with the worst impact first. When segmenting the chromosomes into gene loci, you can use the union of all transcripts of a gene, adding some predefined distance, rather than selecting a single "best" transcript.</p> <p> -That being said, the main gene tracks have tables that try to take guess the most interesting +That being said, the main gene tracks have tables that try to guess the most interesting transcript per gene. For the knownGene tracks (UCSC genes on hg19, Gencode on hg38 and mm10), data tables called "knownCanonical" are available for many assemblies. They try to select only a single transcript/isoform per gene, if possible and for RefSeq similar options exist.</p> <p> <b>UCSC Genes on hg19</b>: 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> <b>Gencode on hg38/mm10</b>: For hg38, the knownCanonical table is a subset of the <a target="_blank"