Missing RefSeq genes from igv

[Amy Hansen]

Hello, i was wondering if there was a way to add or update refseq genes to igv? A gene which is annotated as such in the UCSC genome browser, does not show in the igv RefSeq genes panel. 

Thanks for your help,

Amy 

[Dario Strbenac]

What is the name of that gene ?

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[Dario Strbenac]

Actually, I have an example. For hg19, there is one isoform of GAPDH instead of 2, for the RefSeq annotation.

[Jim Robinson]

I will update the annotation.   In the meantime,  the file I use for UCSC organisms is  "refGene.txt.gz",  for hg19 its at http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz.   You can just download this  file and load it from the file menu,  no need to gunzip it.

Jim

[Maely Gauthier]

Hi Jim,
Should we always expect some annotations differences between the refGene.txt.gz annotation you point to in the post above and the one displayed by IGV? There seems to be an extra exon for isoform 3 of TNFRSF1A reported on UCSC RefSeq that is not shown on IGV (NM_001346092 - exon 6 - chr12:6437923-6451283).


Cheers
M

[James Robinson]

It would not be surprising to find small changes, the UCSC file is updated frequently.   IGV is updated sporadically.   The latest file is always the ucsc url.

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[Maely Gauthier]

Thanks Jim for clarifying.
M

On Tuesday, June 6, 2017 at 2:06:52 PM UTC+9:30, Jim Robinson wrote:

It would not be surprising to find small changes, the UCSC file is updated frequently.   IGV is updated sporadically.   The latest file is always the ucsc url.

On Mon, Jun 5, 2017 at 5:14 PM, Maely Gauthier <maelyg...@gmail.com> wrote:

Hi Jim,
Should we always expect some annotations differences between the refGene.txt.gz annotation you point to in the post above and the one displayed by IGV? There seems to be an extra exon for isoform 3 of TNFRSF1A reported on UCSC RefSeq that is not shown on IGV (NM_001346092 - exon 6 - chr12:6437923-6451283).


Cheers
M

On Wednesday, October 17, 2012 at 1:14:23 AM UTC+10:30, Jim Robinson wrote:

I will update the annotation.   In the meantime,  the file I use for UCSC organisms is  "refGene.txt.gz",  for hg19 its at http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz.   You can just download this  file and load it from the file menu,  no need to gunzip it.

Jim

On Monday, October 15, 2012 9:00:17 PM UTC-4, Dario Strbenac wrote:

Actually, I have an example. For hg19, there is one isoform of GAPDH instead of 2, for the RefSeq annotation.

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