fae1d301198673ede88229892fe5d7bbe76bf3ff max Mon Jul 8 11:49:12 2019 -0700 adding mouse to gencode section in the genes FAQ, no redmine ticket, this came up during a group meeting diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 92f6ed4..16bafcc 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -223,50 +223,50 @@ transcripts than Ensembl/GENCODE transcripts. Also, RefSeq transcripts have their own sequences independent of the genome assembly, so certain population-specific variants may be in RefSeq that are entirely missing from the reference genome sequence. This has the important implication that the position of genome variants are harder to map to RefSeq transcripts than for GENCODE since RefSeq transcripts can have additional sequence or missing sequence relative to the genome.

The links from either transcript model to other gene-related databases are 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. -

For the human assembly hg19/GRCh37: What is the difference between UCSC +
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?

The "UCSC Genes" 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.

The "GENCODE Gene Annotation" track contains data from all versions of GENCODE. "Ensembl Genes" track contains just a single Ensembl version. See the previous question for the differences between Ensembl and GENCODE.

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For the human assembly hg38/GRCh38: What are the differences between the "GENCODE" and +
For the human assembly hg38/GRCh38 and mouse mm10/GRCm38: What are the differences between the "GENCODE" and "All GENCODE" tracks?

"GENCODE" 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 information is also available using the Table Browser. This GENCODE track is updated periodically to match the latest GENCODE release. "All GENCODE" is a super-track that contains all versions of GENCODE as sub-tracks, but these tracks have less third-party information. Sub-tracks are never removed from "All GENCODE", and new sub-tracks are added as there are additional GENCODE releases.

What is the difference between "GENCODE Comprehensive" and "GENCODE Basic"?