IGV Running with no internet connection

[Lisa Lattarulo]

I know this is unheard of, but I have a computer with no internet connection that I am trying to get IGV running on.  I have it running, but I am unable to get it to accept new reference genome files.  I have the human_g1k_v27_decoy.fasta (and .fai index) copied onto my computer.  I used Genomes->Load Genome From File and selected the .fasta file.  It says that the genome is loaded, the bottom left says "4 tracks loaded" (or something similar, I don't have the computer in front of me right now) but there is no sequence information loaded.  The entire screen is blank (except for the light gray dividing lines).  I get the same result if I try Genomes->Create .genome File and select my .fasta that way.  Is there some other step that I am missing?  Do I have to put the .fasta files in a certain location?  Thank you for any insight you may be able to provide. 
Lisa

[Helga Thorvaldsdottir]

Lisa,

You won't see the actual sequence if the view is zoomed out too far. Have you tried zooming in?

Helga

On 4/12/16 1:29 PM, Lisa Lattarulo wrote:

I know this is unheard of, but I have a computer with no internet connection that I am trying to get IGV running on.  I have it running, but I am unable to get it to accept new reference genome files.  I have the human_g1k_v27_decoy.fasta (and .fai index) copied onto my computer.  I used Genomes->Load Genome From File and selected the .fasta file.  It says that the genome is loaded, the bottom left says "4 tracks loaded" (or something similar, I don't have the computer in front of me right now) but there is no sequence information loaded.  The entire screen is blank (except for the light gray dividing lines).  I get the same result if I try Genomes->Create .genome File and select my .fasta that way.  Is there some other step that I am missing?  Do I have to put the .fasta files in a certain location?  Thank you for any insight you may be able to provide. 
Lisa

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[Lisa Lattarulo]

Ok wow...I can't believe I didn't see that.  I'm sorry.  But, now that I can see the sequence I am having another issue.  When I am using the FASTA file, and zoom into a particular location (for example the STR CSF1PO at 5:149455887-149455938) everything looks like I would expect - I can see the TCTA repeat.  But, when I am using the reference that I created the .genome file for when I zoom into that same area I no longer see a repeating sequence and the reference sequence does not match what I see on the UCSC genome browser (or the original FASTA).  It seems like an index file problem?  I have the index file in the same folder though.  Is there something else it could be?  Does the human_g1k_v37_decoy.fasta file need an alias file for chromosome names or anything?  Thank you!

Lisa

[Jim Robinson]

Hi,  this would indicate that your reference sequence (i.e. fasta file) differs from whatever you are comparing it to.   I can't see anyway this could be caused by an index.     Where did you copy your fasta and index from?

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[Lisa Lattarulo]

Thank you for getting back to me.  As of right now I think it is working correctly with the fasta.  I got it out of my genomes folder after doing a download of the human 37 decoy sequence from IGV (from a computer that is attached to the internet).  Thanks again.