4fabe6e7b2e485192b45e9ea0efbb86e7f96e872 max Thu Dec 3 00:40:11 2020 -0800 fixing the FAQ section about single transcript display, now pointing to the next section, refs #26617 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 772bd17..e924873 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -449,34 +449,33 @@ <h2>How can I show a single transcript per gene?</h2> <p> For the tracks "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg19&g=knownGene">UCSC Genes</a>" (hg19) or "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=knownGene">GENCODE Genes</a>" (hg38), click on their title and on the configuration page, uncheck the box "Show splice variants". Only a single transcript will be shown. The method for how this transcript is selected is described in the next section below and in the track documentation. </p> <p class='text-center'> <img class='text-center' src="../images/SpliceVariants.png" 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> +For the various single-transcript options of "NCBI RefSeq", please +see the discussion of "single transcript" tracks in the next section. </p> <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>