UCSC known genes

[GIOVANNA MIGLIORELLI]

Dear Support,

I'm interested in the UCSC pipeline leading to Known gene set. I found it interesting your benchmarking against refseq and Ensembl but the paper reporting it is a bit dated:

https://doi.org/10.1093/bioinformatics/btl048

the question is: is the pipeline still mantained and up to date? If it is the case, is there any updated resource I can have access to, relating the pipeline (e.g. paper, statistics, benchmarking)?

Thanks for the usual excellent support 

[Daniel Schmelter]

Hello Giovanna,

Thank you for your question about the knownGene annotation pipeline.

The knownGene pipeline is no longer maintained and has been functionally replaced by the GENCODE Comprehensive gene sets. You can see this most clearly in the hg38 and mm10 genomes where it has been fully replaced. The knownGene track for hg19 remains in place as a legacy track, last updated in 2013. We recommend using the most recently updated GENCODE gene set instead (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV31lift37).

For reference purposes, the paper you sent contains the most complete description of the knownGene pipeline aside from the track description itself (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene). Confirmation that the software is no longer in use can be found in our FAQgenes help page (http://genome.ucsc.edu/FAQ/FAQgenes.html).

I hope this was helpful. If you have any more questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,
Daniel Schmelter
UCSC Genomics Institute

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