310b7abb097f8f50d28eaca8149577b0f412e731 max Fri Jul 2 06:46:42 2021 -0700 more fixes for the genes faq page, refs #27778 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 9ed54e4..c931a0e 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -515,44 +515,49 @@ (that is to say, one canonical isoform per ENSEMBL gene ID), and the method of choosing the isoform is described as such:</p> <p style="margin-left: 10em"> <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> <p> -<b>NCBI RefSeq (hg19/hg38)</b>: NCBI manually selects few, usually one, +<b>NCBI RefSeq (hg19/hg38)</b>: On this track, there are three subtracks with slightly +different aims, all of which show only a single transcript (or less) for each gene. +<ul> + <li> RefSeq Select: 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 +is available in the RefSeq Select track under NCBI RefSeq. +<li>MANE: RefSeq and the EBI 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 +<li>HGMD: For the special case of clinical diagnostics where an even more reduced number of transcripts simplifies visual inspection, 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 to which all reported clinical variants can be mapped to. +the transcript is the one to which all reported HGMD clinical variants can be mapped to. +</ul> <a name="whatdo"></a> <h2>This is rather complicated. Can you tell me which gene transcript track I should use?</h2> <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