Which track represents IGV dm3 genome annotation

[Koustav Pal]

Hi.

The IGV website contains no information regarding the mapping between UCSC tables and the available genome annotation on their servers. Can you guys clear the air regarding this confusion in the context of dm3? 

The only information I have is this, the dm3 IGV gene track corresponds to the UCSC dm3 2006 release. But it is not clear which exact tables on UCSC does this gene track correspond to. 

Let me know if I should contact IGV support directly regarding this query.

Koustav Pal, 

PhD student in Computational Biology,

Francesco Ferrari's group,

IFOM- The FIRC Institute of Molecular Oncology

Milano, Italy.

[Christopher Lee]

Hi Koustav,

Thank you for your question about which UCSC table corresponds to IGV
Gene tracks on dm3. You will need to ask IGV for an official answer,
but here is how I found this information out for dm3.

First I opened IGV and downloaded the dm3 genome via the "More" link
from the genome list dropdown in IGV. Then, using this igv-help google
forum thread as a guide:
https://groups.google.com/d/msg/igv-help/y5-yJHqYkvc/QSkendcaaCAJ

I navigated to my ~/igv/genomes directory, unzipped the dm3.genome
file, and looked at the property.txt file:

$ cd ~/igv/genomes
$ unzip dm3.genome
$ cat property.txt
id=dm3
ordered=true
name=D. melanogaster (dm3)
cytobandFile=D._melanogaster_dm3_cytoband.txt
geneFile=refSeq.dm3.genepred
chrAliasFile=dm3_alias.tab
sequenceLocation=http://www.broad.mit.edu/igv/sequence/dm3

Which seems to indicate that IGV is using the UCSC RefSeq Genes track
as it's default gene track. However, if you look at dm3 in our
browser:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=dm3&hideTracks=1&refGene=pack

You will see that there are differences between the annotation we
display and the IGV annotation. From this igv-help thread:
https://groups.google.com/d/msg/igv-help/qDTXaVC3CIs/hwfwHPC-4-IJ

It appears that IGV does not regularly update the gene annotations.
You can download the updated annotation from our download server here:
http://hgdownload.cse.ucsc.edu/goldenPath/dm3/database/refGene.txt.gz

Please let us know if you have further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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