HG19 genome

answered 2013-02-16 04:46:48 -0600

Nick Schaefer
1 ●2 ●2 ●2

OK, problem solved. My Avira antivirus program was the culprit. Switched it off and the Refseq came down fine.

answered 2013-02-07 21:46:40 -0600

Nick Schaefer
1 ●2 ●2 ●2

Hi Gabe, When I do a Refresh under the Annotations tab I still get the same ! error message. The tooltip says: Connection timed out. Please check your network and proxy settings.

It takes about 6 secs for the ! error message to appear after hitting the Refresh.

I'm using the W7/64 version of GenomeBrowse

answered 2013-02-07 09:01:13 -0600

Gabe Rudy
90 ●1 ●4 ●6 http://blog.goldenhelix.c...

Hey Nick,

That's something we haven't run into, where you are able to download one of the example RNA-Seq samples but not annotations.

The "rfs://" versus "http://" is just protocol details but both the example samples and annotations are being served from the same host in the same manner (which is over HTTP port 80).

Could you double check that when on the Annotations tab, hitting the Refresh button doesn't pull in the source list for data.goldenhelix.com?

When you hover over the top level node that has the error, it should also display a tooltip with the details of why it was not able to connect. If you could post that as well it might help troubleshoot the issue.

Thanks!

answered 2013-02-07 09:00:52 -0600

Gabe Rudy
90 ●1 ●4 ●6 http://blog.goldenhelix.c...

Hey Nick,

That's something we haven't run into, where you are able to download one of the example RNA-Seq samples but not annotations.

The "rfs://" versus "http://" is just protocol details but both the example samples and annotations are being served from the same host in the same manner (which is over HTTP port 80).

Could you double check that when on the Annotations tab, hitting the Refresh button doesn't pull in the source list for data.goldenhelix.com?

When you hover over the top level node that has the error, it should also display a tooltip with the details of why it was not able to connect. If you could post that as well it might help troubleshoot the issue.

Thanks!

answered 2013-02-05 22:30:47 -0600

Nick Schaefer
1 ●2 ●2 ●2

Jami, Still having problems with the reference sequence download. I'm wondering whether the rfs://data.goldenhelix.com:80/rfs/ source is a problem. I don't yet have a BAM file of my own but did download the example sample BT-20_12.5M which shows up in the browser OK. I notice this is sourced via http// not rfs//. The CEPH 1463 trio example is another that uses rfs// and is highlighted with an!.

I have added GenomeBrowse to my firewall exceptions and restarted the computer.

The proxy settings I'm not so sure about. I've set it to Automatic in GenomeBrowse.

thanks

Nick

answered 2013-02-05 14:18:36 -0600

Jami Bartole
201 ●3 ●3 http://www.goldenhelix.co...

Hi Nick,

I am sorry you are having trouble with GenomeBrowse.

When the Annotations tab reports "! data.goldenhelix.com (showing 0/0)" that means GenomeBrowse is not able to access our annotation servers and as a result will not prompt you to download the reference sequence because it is not accessible.

There are a couple of options to attempt to fix the issue. One is to hit the Refresh button at the bottom of the Annotations tab. If that does not give GenomeBrowse access to the server you may need to reset your proxy settings.

You can access your proxy settings by going to Tools > Proxy Settings. If you know the settings you can enter them in manually or select Automatically detect proxy settings and GenomeBrowse may be able to determine them.

If neither of those options fix the issue your firewall may be blocking the connection and you may need to manually give GenomeBrowse assess to data.goldenhelix.com through the firewall.

Please let us know if we can help further.

Thanks, Jami...

answered 2013-02-04 23:13:11 -0600

Nick Schaefer
1 ●2 ●2 ●2

Hi Jami, I have a similar problem. I have installed the browser but never saw a dialog box asking to download the ref seq as shown in the help video. I've looked under annotations and there's a "! data.goldenhelix.com (showing 0/0)" comment. What am I doing wrong?

Nick

answered 2013-01-31 09:11:45 -0600

Jami Bartole
201 ●3 ●3 http://www.goldenhelix.co...

Hi Anthony,

We currently have two separate reference sequence tracks that correspond to the hg19 human build. It is recommended that you download both of them to avoid the reference sequence error (code 18) that you received when loading your BAM file.

The first build is the GRCh_37 build that was curated from data obtained from UCSC and the second is the GRCh_37_g1k build that was curated from 1000Genomes data. These builds differ slightly most prominently in the mitochondrial region so GenomeBrowse considers them separate human builds that correspond to hg19.

The GRCh_37_g1k build was just made available yesterday when version 1.0.7 of GenomeBrowse was released for download. If you update to this build GenomeBrowse should automatically prompt you to download the corresponding reference sequence when you load your BAM file.

You can update GenomeBrowse by downloading the current version from our website.

You can also download the track from the Add dialog under the Annotations tab. To make this build visible you will need to uncheck the option at the bottom of the dialog to "Hide sources for genomes other than...". The track is called Reference Sequence, 1000Genomes and the build is GRCh_37_g1k.

Please let us know if you have any further questions.

Thanks, Jami...