GENE ANNOTATION MISSING

[Varun Gupta]

Hi,
I am using Zebra fish genome and was looking for the gene called ARSI, but IGV does not show this gene. Why so??
GENOME : GRCz10/danRer10

I looked into ensembl data base and it is present there.

Thanks
Regards
Varun

[Jim Robinson]

Is it present in the refseq set from UCSC?  That is the set we use for annotations.

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[VG]

Hi Jim,

I looked for that gene on UCSC browser and I cannot find it. Thanks for the help. Can you also tell me how to extract the refseq set from UCSC for Zebra fish for known genes. I know it is by default loaded when we load the genome.

Thanks

Varun

On Mon, Aug 22, 2016 at 4:59 PM, Jim Robinson <jrob...@broadinstitute.org> wrote:

Is it present in the refseq set from UCSC?  That is the set we use for annotations.

On 8/22/16 1:29 PM, Varun Gupta wrote:

Hi,
I am using Zebra fish genome and was looking for the gene called ARSI, but IGV does not show this gene. Why so??
GENOME : GRCz10/danRer10

I looked into ensembl data base and it is present there.

Thanks
Regards
Varun

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[Jim Robinson]

There are various files ready for download here, many can be loaded directly into IGV.  If you give me a list of these files you'd like I will try adding them,  but don't say "all of them" my time for this is limited:

http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/

You can also use the table browser and extract annotations in "bed" format.  Be sure to name the file to end in ".bed".

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