10c3680ae0bc23f666f067f473249a6008d0cecd dschmelt Tue Sep 3 15:07:02 2019 -0700 Removing sentence about us considering to continue knwonGene pipeline refs#24069 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 9a29c47..1d8566c 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -231,32 +231,31 @@ different. In general, it seems that high-throughput sequencing data results, e.g. RNA-seq, are often using Ensembl/GENCODE annotations and human genetics results are reported using RefSeq annotations. It depends on your particular project which gene model set you want to use. Over time, the two transcript databases have been and are becoming more similar. <a name="hg19"></a> <h6>For the human assembly hg19/GRCh37 and mouse mm9/NCBI37: What is the difference between UCSC Genes, the "GENCODE Gene Annotation" track and the "Ensembl Genes" track?</h6> <p>The "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg19&g=knownGene">UCSC Genes</a>" track, also called "Known Genes", is available only on assemblies before hg38. It was built with a gene predictor developed at UCSC. This gene predictor uses protein, EST and cDNA annotations to derive a relatively restricted gene transcript set. The software is no longer in use and there are no plans to release the track on newer human assemblies. It was last used for the -mm10 mouse assembly. We are considering updating the hg19 annotation produced by this -software and are interested in any user feedback on the topic.</p> +mm10 mouse assembly.</p> <p>The "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeSuper">GENCODE Gene Annotation</a>" track contains data from all versions of GENCODE. "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg19&g=ensGene">Ensembl Genes</a>" track contains just a single Ensembl version. See the previous question for the differences between Ensembl and GENCODE. </p> <a name="hg38"></a> <h6>For the human assembly hg38/GRCh38 and mouse mm10/GRCm38: What are the differences between the "GENCODE" and "All GENCODE" tracks?</h6> <p> "<a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=knownGene">GENCODE</a>" is the default gene track on hg38 (similar to "Known Genes" on hg19), which means that it is associated with a large amount of third party information when you click on a gene. This related