Problems with an alias file

[Patricia Pukkila]

I tried to follow the instructions to create a chromosome name alias file (attached), and I put a copy in my /igv/genomes folder.  However, after launching, IGV2.1 did not proceed past a blue screen.  When I renamed the file ccinv3_alias.tab.txt or ccinv3_alias.txt, IGV2.1 opened fine, but I received an error message saying that the bam file I am trying to view (which uses the gb identifiers) does not contain any sequence names matching the current genome.  My alias file does not contain entries for "chromosomes" 68-14 of the assembly, since I don't really care about those at this point.  I note that the error message begins with chromosome 68, but I just assumed it would continue through the alias file until it found a match.  I would appreciate any help you can offer, thanks!! 

[Jacob Silterra]

Hi Patricia,

The alias file looks good. Could you attach your "igv.log" file? It should be in the igv.folder. I'll be emailing you instructions for uploading the files you're looking at to our FTP site so I can try to reproduce the problem.

Thanks,
-Jacob

[Jacob Silterra]

I corresponded with you off list, but am rewriting here for posterity. The issue was one of documentation. As of this email, the instructions for creating an alias file were at http://www.broadinstitute.org/igv/LoadData. The user created an alias file according to those instructions, and aliases were not loaded. When they reversed the column names, aliases were loaded properly.

It's not clear to me whether the documentation is confusing or simply incorrect, it may be that you were using alias files differently than we expect. Regardless, the documentation needs to be more clear and cover all cases. Thanks for bringing this to our attention.

-Jacob

On Wed, Jun 13, 2012 at 3:08 PM, Patricia Pukkila <puk...@unc.edu> wrote:

I tried to follow the instructions to create a chromosome name alias file (attached), and I put a copy in my /igv/genomes folder.  However, after launching, IGV2.1 did not proceed past a blue screen.  When I renamed the file ccinv3_alias.tab.txt or ccinv3_alias.txt, IGV2.1 opened fine, but I received an error message saying that the bam file I am trying to view (which uses the gb identifiers) does not contain any sequence names matching the current genome.  My alias file does not contain entries for "chromosomes" 68-14 of the assembly, since I don't really care about those at this point.  I note that the error message begins with chromosome 68, but I just assumed it would continue through the alias file until it found a match.  I would appreciate any help you can offer, thanks!! 

--
Jacob Silterra
Software Engineer
Broad Institute