2178fc298d3dd0cb7e400ccd0d944c5132b6026f lrnassar Mon Mar 18 17:01:48 2019 -0700 Minor changes to unreleased FAQgenes ref#22696 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 74e757a..f33ca1e 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -263,41 +263,41 @@ <a name="ccds"></a> <h6>What is CCDS?</h6> <p> The <a target=_blank href="https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi"> Consensus Coding Sequence Project</a> is a list of transcript coding sequence (CDS) genomic regions that are identically annotated by RefSeq and Ensembl/GENCODE. CCDS undergoes extensive manual review and you can consider these a subset of either gene track, filtered for high quality. The CCDS identifiers are very stable and allow you to link easily between the different databases. As the name implies, it does not cover UTR regions or non-coding transcripts. </p> <a name="justsingle"></a> <h6>How can I just show a single transcript per gene?</h6> <p> For the tracks "<a target=_blank -href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene">UCSC Genes</a>" +href="../cgi-bin/hgTrackUi?db=hg19&g=knownGene">UCSC Genes</a>" (hg19) or "<a target=_blank -href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene">GENCODE Genes</a>" +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 track documentation below the configuration settings.</p> <p>For the track <a target=_blank -href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite"> -NCBI RefSeq</a> (hg38), you can activate the subtrack "RefSeq Clinical". +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="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 all possible transcripts, GENCODE provides a comprehensive gene set. For human genetics or variant annotation, a more restricted transcript set is usually sufficient and "NCBI RefSeq" is the standard. If you are only interested in protein-coding annotations, CCDS or UniProt may be an option, but this is rather unusual. </p> <p> For manual inspection of exon boundaries of a single gene, and especially if it