IGV .genome files: where is the sequence?

[pmiguel]

IGV offers a number of "built in" genomes to display your .bam file against. These are apparently packaged in .genome files. The .genome file is actually a zipped set of a few files. But none of them seem to be the actual genome sequence.

Where does IGV keep the genome sequence?

For example, the chicken genome reference file, "galGal3.genome" after unzipping, via "ls -1s"

3 Chicken_galGal3_cytoband.txt
1514 chicken.refflat
3 property.txt
1755 refGene.txt

None of them contain the chicken reference sequence.

--
Phillip

[hanifk]

IGV offers a number of "built in" genomes to display your .bam file against. These are apparently packaged in .genome files. The .genome file is actually a zipped set of a few files. But none of them seem to be the actual genome sequence.

Where does IGV keep the genome sequence?

For example, the chicken genome reference file, "galGal3.genome" after unzipping, via "ls -1s"

3 Chicken_galGal3_cytoband.txt
1514 chicken.refflat
3 property.txt
1755 refGene.txt

None of them contain the chicken reference sequence.

--
Phillip

I am curious that how did you find galGal3.genome is a zip file.
I also don't know where the sequence is.
waiting reply...

[pmiguel]

I am curious that how did you find galGal3.genome is a zip file.
I also don't know where the sequence is.
waiting reply...

You would have to ask Rick Westerman, he determined the file was zipped. He looked at the first few characters of the file and saw "PK" there. That said, when I look now, I see no "PK".

IGV has fairly extensive documentation, so it is probably mentioned somewhere.

--
Phillip

[pmiguel]

Not exactly an answer, but should be suitable for my purposes. The Broad describes the source of each .genome file it has "built in":

http://www.broadinstitute.org/igv/Genomes

--
Phillip

[dawe]

I believe built-in genomes are read/cached from Broad website... I had an error message yesterday using IGV, it warned me that communication with the main server has been interrupted. As results, DNA sequences (and translated proteins) disappeared.
If you build your own genome, instead, you should find a directory like

IGV_Genomes/
|
+-MyGenome/
   |
   +-MyGenome.genome
   +-MyGenome.genome_seq/
      |
      +-OriginalSequenceFile

d

[seqfast]

@pmiguel

if you're on a unix/linux system, type:

file galGal3.genome

this will tell you (within certain limits) what type of file - ascii, binary, zip, gzip etc.

not sure for windows. should work on command line on a mac

-sf

[pmiguel]

@seqfast,

It works:
file galGal3.genome
galGal3.genome: Zip archive data, at least v2.0 to extract

Thanks!

--
Phillip

[ykingh]

This thread helps.