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2013-02-21 00:42:21 -0600 answered a question Finding and loading external annotation tracks

Oops, my antivirus program again. Just doesn't like the rfs address I guess. I've discovered in the fine print that I can't make exceptions in the 64bit version. Anyway I've downloaded those tracks now. thanks Nick PS I really like this browser-great visualisation. A lot of fun as well as educational.

2013-02-20 12:37:04 -0600 asked a question Finding and loading external annotation tracks

How do I find and load external annotation tracks such as OMIM and RefSeq data? Eg as mentioned in Gabe's video and the GenomeBrowse web page.

2013-02-19 17:43:01 -0600 answered a question How to use DTC genotype data?

Thanks Jami, I look forward to importing VCFs. Hopefully the genotype data won't be far behind as they have very similar structure to VCF.

Nick

2013-02-18 15:05:08 -0600 asked a question How to use DTC genotype data?

Is it possible for the downloaded raw genotype results from companies like 23&Me or FTDNA to be used as a comparison track when looking at say exome data (BAM files)? I realise that a lot of it is intron/intergenic.

2013-02-16 04:46:48 -0600 answered a question HG19 genome

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

2013-02-15 21:14:25 -0600 answered a question HG19 genome

Hi Jami and Gabe, I'm wondering whether you have any further suggestions? I also tried the Win 7/ 32 bit but same problem. Am I right in thinking that the full Ref Seq data is never downloaded as such but there is continual communication between my computer and your server when one zomms in or along the genome? I'm wondering whether there is speed/communication problem via your Remote File System? I'm in Australia on ADSL1 running at about 6MB down 0.3MB up.

In Tools if I don't select Austomatic for the Server what other choices are there?

Thanks

Nick PS Would there be any point in going down to the local coffee shop and bypassing my own ISP? I did try using a usb modem dongle as an alternative to going through my own modem/router but same problem with the Ref Seq.

2013-02-07 21:46:40 -0600 answered a question HG19 genome

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

2013-02-05 22:30:47 -0600 answered a question HG19 genome

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

2013-02-04 23:13:11 -0600 answered a question HG19 genome

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