EquCab3
Roach, Jessica
Hello –
I am looking to load the EquCab3 build in to Illumina’s GenomeViewer - in the Genome Studio software. I have followed their User Framework document but it seems the files required for this aren’t yet available from your site. Specifically the files:
chromInfo.txt.gz
refGene.txt.gz
refSeqSummary.txt.gz
And then all the data set by Chromosome.
(Ideal but not essential: cytoBand.txt.gz, knownGene.txt.gz, knownToRefSeq.txt.gz, cpgIslandExt.txt.gz)
I spoke to them about it as thought it was user error from my end as I am new to this and they suggested I contact you directly. Is this something you are going to be building in the future? Any help or guidance would be hugely appreciated.
Best wishes,
Jess
Jessica Roach BVetMed MRCVS
PhD Student
Royal Veterinary College
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Hiram Clawson
You will find most of the files you mention in the download directory:
https://hgdownload.soe.ucsc.edu/goldenPath/equCab3/database/
the refSeqSummary.txt.gz file can be found in:
https://hgdownload.soe.ucsc.edu/goldenPath/hgFixed/database/
There are no knownGene files for equCab3, such files are found
only in databases: hg19, hg38, mm10.
You can use the cytoBandIdeo.txt.gz file in place of the cytoBand.txt.gz
--Hiram
On 11/11/20 1:42 AM, Roach, Jessica wrote:
> Hello -
> I am looking to load the EquCab3 build in to Illumina's GenomeViewer - in the Genome Studio software. I have followed their User Framework document but it seems the files required for this aren't yet available from your site. Specifically the files:
> chromInfo.txt.gz
> refGene.txt.gz
> refSeqSummary.txt.gz
> And then all the data set by Chromosome.
> (Ideal but not essential: cytoBand.txt.gz, knownGene.txt.gz, knownToRefSeq.txt.gz, cpgIslandExt.txt.gz)
>
> I spoke to them about it as thought it was user error from my end as I am new to this and they suggested I contact you directly. Is this something you are going to be building in the future? Any help or guidance would be hugely appreciated.
>
> Best wishes,
> Jess
>
> Jessica Roach BVetMed MRCVS
> PhD Student
> Royal Veterinary College
>
>