841bc0ee887c7f5788a8be42094df6c1f922d24e max Fri Jan 17 05:48:48 2020 -0800 tiny fix to genes FAq, refs #24780 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 82dfb94..47da356 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -454,38 +454,39 @@ 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> <p> <b>NCBI RefSeq (hg19/hg38)</b>: NCBI manually selects few, usually one, transcript per gene called "RefSeq Select", based on <a target=_blank href="https://www.ncbi.nlm.nih.gov/refseq/refseq_select/">various criteria</a>. Example use cases are comparative genomics and variant reporting. This subset is available in the RefSeq Select track under NCBI RefSeq. RefSeq and the EBI -also select one transcript for every protein coding gene, a project called <a +also select one transcript for every protein coding gene that is annotated exactly +the same in both Gencode and RefSeq, a project called <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2019/03/12/mane-select-v0-5/" target=_blank>"MANE select"</a>, which is another subtrack of NCBI RefSeq. For the special case of clinical diagnostics where an even more reduced number of transcripts simplifies visual inspection, -we also provide "RefSeq HGMD", another subtrack of NCBI RefSeq. It contains +we also provide another subtrack, "RefSeq HGMD". It contains (usually) a single transcript only for genes known to cause human genetic diseases and -the transcript is the one where reported clinical variants can be mapped to. +the transcript is the one to which all reported clinical variants can be mapped to. <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 one of the most comprehensive gene sets. 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. If you are interested in the best splice site coverage, AceView is worth a look. </p> <p> For manual inspection of exon boundaries of a single gene, and especially if it