Mirroring of Genome browser seems to be broken
Nagaraj Selvaraj-External
Hi Team,
Hope you are doing good.
I am part of Regeneron’s infrastructure team.
We have mirrored the UCSC genome browser (https://genome.ucsc.edu/index.html) on to our environment.
We found the mirroring to be inaccurate.
The below screenshot is from your website. you have GENCODE V43 here.
In our environment, we have Gencode V32.
How should we update it to have v43 in our environment. As well.
Regards,
Nagaraj Selvaraj
Infrastructure Engineer
Digital Technologies & Engineering
Regeneron Pharmaceuticals
1 Rockwood Rd; Sleepy Hollow, NY 10591 - USA
REGENERON
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Gerardo Perez
Hello, Nagaraj.
Thank you for your interest in the Genome Browser and for your question about updating to GENCODE V43.
The GENCODE track can be updated by ensuring the following tables and /gbdb files are up-to-date:
kgXref
knownGene
knownGeneExt
knownGeneMrna
knownGenePep
ceBlastTab
dmBlastTab
drBlastTab
foldUtr3
foldUtr5
gnfAtlas2Distance
gnfU95Distance
humanHprdP2P
humanVidalP2P
humanWankerP2P
kgAlias
kgColor
kgProtAlias
kgSpAlias
kgTargetAli
kgV41ToKgV43
knownAlt
knownAttrs
knownBlastTab
knownCanonical
knownCds
knownIsoforms
knownToEnsembl
knownToGencodeV43
knownToGnfAtlas2
knownToHprd
knownToLocusLink
knownToMrna
knownToMrnaSingle
knownToMupit
knownToPfam
knownToRefSeq
knownToSuper
knownToTag
knownToU133
knownToU95
knownToVisiGene
knownToWikipedia
mmBlastTab
pfamDesc
rnBlastTab
scBlastTab
scopDesc
spMrna
ucscGenePfam
ucscScop/gbdb/hg38/gencode/gencodeV43.bb
/gbdb/hg38/knownGene.ix
/gbdb/hg38/knownGene.ixx
/gbdb/hg38/targetDb/hg38KgSeqV43.2bit
/gbdb/hg38/knownGeneFastV43.ix
/gbdb/hg38/knownGeneFastV43.ixx
Let us know if you need help locating the files.
I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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