IGV not displaying bases

[adam harmon]

IGV is not displaying any of the bases on the tracks, neither the when it would just display SNP or when i select " show all bases". all i see are the tracks( which are colored appropriately) which display the insertions and deletion correctly.

any help would be greatly appreciated. i have version 2.1.12.

[Jim Robinson]

What do you see when you zoom all the way in in the sequence track?  Is sequence there?    Also, it would be helpful to see the details of one of your reads,  which you can get by right clicking over a read and selecting "Copy read details to clipboard".

Jim

[adam harmon]

i have found out what was going  on. apparently my genomes have gotten changed in someway and IGV didn't see any sequencing information i the files. So i used a backup and copied over the .genome files and it began displaying the bases appropriately. thank you for your help.

[Murat Uenalan]

I currently ran into the same problem. As use the online version and its quite difficult to translate your solution. 

I am running ubuntu 12.10. Is there may be a hidden folder where the cached .genomes are stored ? Any suggestion is very welcome !

[Jacob Silterra]

The cached genomes are stored in the <igv directory>/genomes. By default the IGV directory is in <your home folder>/igv, you can view where it's set at View -> Preferences -> Advanced -> IGV directory (at the bottom).

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Jacob Silterra
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Broad Institute

[Jim Robinson]

Murat, 

Are you having a problem with your own (imported) genomes, or with genomes we host?  

Jim

[Murat Uenalan]

Jim,

Its the genomes you host. Although i cleared the genome cache (via the preference dialogue; thx!), the base sequence is still not displayed; and the SNP's are not shown either ?!

I suppose it has to do with 

   Error reading genome sequence from: http://igv.broadinstitute.org/genomes/seq/hg19/chr2.txt

in my igv.log (attached). I already posted it separately here today.

Thx for the help,

Murat

[Jim Robinson]

Could you try accessing that URL through a web browser? I'm not having
any problems accessing it, of the server is here where I work.

[Murat Uenalan]

Indeed,

It failed from my work computer. Now at home I come through; Puh, that is odd. I will try that from work tomorrow again.

Thx so far,
Murat

[Jim Robinson]

Is there perhaps a new firewall or proxy at work that is blocking access
to our server?

Jim

[Murat Uenalan]

According to our network service team, it is subject to virus checks and need 10 minutes to be served ! So it seems

that it is indeed specific to my work network. IGV obviously timeouts after seconds.

Is there any workaround for me ? Maybe store the files into a local path ? That might also speed-up things for me ?

Thank you for taking the time,

Murat

[Murat Uenalan]

Update:

chr2.txt is opened by IGV for http streaming?, but our Sophos Security Proxy does not support that and blatantly downloads the full 243.2MB for serving it. According to our

vendor, since december there was no update. 

Can this be due to some java update ? Anyway, a workarround would be superb !

Thx,

Murat

Am Montag, 4. Februar 2013 20:01:13 UTC+1 schrieb Jim Robinson:

[Jim Robinson]

The files are served by http, however they are accessed by IGV in chunks
as needed using range-byte requests. I interpret your message to mean
that the proxy is stripping the range-byte header off the request. If
this has worked in the past perhaps the administrator has changed some
settings? This is usually configurable, I don't know this particular
proxy.

However, we do test for this condition and work around it internally, I
would like to know why the test failed. Could you send your igv.log
file to igv-...@broadinstitute.org?

The straightforward workaround is to define you own genome locally and
use that following the instructions in the user guide. You'll need the
fasta, you can get it from UCSC, but I will post it for download
later today and send you instructions.

Jim

[Jim Robinson]

The files are served by http, however they are accessed by IGV in chunks
as needed using range-byte requests. I interpret your message to mean
that the proxy is stripping the range-byte header off the request. If
this has worked in the past perhaps the administrator has changed some
settings? This is usually configurable, I don't know this particular
proxy.

However, we do test for this condition and work around it internally, I
would like to know why the test failed. Could you send your igv.log
file to igv-...@broadinstitute.org?

The straightforward workaround is to define you own genome locally and
use that following the instructions in the user guide. You'll need the
fasta, you can get it from UCSC, but I will post it for download
later today and send you instructions.

Jim

[M. Uenalan]

Jim,

This is my igv.log !

Proxy range-byte requests: Our campus network administrators are
debugging via comparing +/- proxy. Anyway, I will try to ask him
testing IGV without proxy.. as he is not willing to lift the security
restrictions for me.

Looking forward for the workarround,
Thx,
Murat




2013/2/5 Jim Robinson <jrob...@broadinstitute.org>:

[Jim Robinson]

OK, thanks for the log. The workaround is to define your own genome
locally as described here
http://www.broadinstitute.org/software/igv/LoadGenome (scroll down to
"creating a .genome file"). For convenience I've placed all the
files you need for hg19 here:
http://www.broadinstitute.org/igv/projects/downloads/hg19.zip. For the
id, use something other than "hg19" to avoid conflicts with our hosted
version, the id is only used internally and in session files.

Jim

[XW Yang]

I have the same problem.

The fasta file should be well-formatted. 

Don't put all the sequences in one line.

Try 60 or 80 letters per line.