genome in session file

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mtr...@mindspring.com

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Apr 3, 2019, 9:00:35 PM4/3/19
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Hello

What is the syntax of specifying a genome to load in a session file?  Up till now I've done this separately but, if possible, I would like to load it via the session file loading the tracks.

Thanks

Mark

James Robinson

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Apr 3, 2019, 9:42:38 PM4/3/19
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See http://software.broadinstitute.org/software/igv/Sessions

The genome attribute can be an id  (e.g. "hg38"),  or a file or url path to a fasta or .genome file.

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Mark Rose

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Jun 3, 2019, 2:34:57 PM6/3/19
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It doesn't seem to work

When I load the session file


Only this session file works (after loading the reference fasta)

<?xml version="1.0" encoding="UTF-8"?>
<Global> genome="OsXa13WT.fa" locus="OsXa13WT.fa" version="3"
<Resources>
<Resource name="L5-50 align" path="http://demeter//scratch-large/3-monthly/GEDI2/CDZYK190510_PCRseq/1558554885/L5-50/delivered/L5-50-vs-OsXa13WT.fa.sort.bam"/>
</Resources>
</Global>

Neither of the following work (reference fasta not loaded)

<?xml version="1.0" encoding="UTF-8"?>
<Global> genome="/scratch-large/3-monthly/GEDI2/CDZYK190510_PCRseq/1558554885/L5-50/delivered/OsXa13WT.fa" locus="OsXa13WT.fa" version="3"
<Resources>
<Resource name="L5-50 align" path="http://demeter//scratch-large/3-monthly/GEDI2/CDZYK190510_PCRseq/1558554885/L5-50/delivered/L5-50-vs-OsXa13WT.fa.sort.bam"/>
</Resources>
</Global>


<?xml version="1.0" encoding="UTF-8"?>
<Global> genome="http://demeter/scratch-large/3-monthly/GEDI2/CDZYK190510_PCRseq/1558554885/L5-50/delivered/OsXa13WT.faOsXa13WT.fa" locus="OsXa13WT.fa" version="3"
<Resources>
<Resource name="L5-50 align" path="http://demeter//scratch-large/3-monthly/GEDI2/CDZYK190510_PCRseq/1558554885/L5-50/delivered/L5-50-vs-OsXa13WT.fa.sort.bam"/>
</Resources>
</Global>





On Wednesday, April 3, 2019 at 9:42:38 PM UTC-4, James Robinson wrote:
See http://software.broadinstitute.org/software/igv/Sessions

The genome attribute can be an id  (e.g. "hg38"),  or a file or url path to a fasta or .genome file.

On Wed, Apr 3, 2019 at 6:00 PM <mtr...@mindspring.com> wrote:
Hello

What is the syntax of specifying a genome to load in a session file?  Up till now I've done this separately but, if possible, I would like to load it via the session file loading the tracks.

Thanks

Mark

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James Robinson

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Jun 3, 2019, 11:21:56 PM6/3/19
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Hi Mark,

I've spent an hour testing all sorts of variants and they all work for me.   Your URL parameter should be uri encoded, but that's probably  not critical here.    If those paths exist  at the path or url provided it should work.    Is there any log output?

I don't think you said but I'm assuming you are using a recent version of IGV.

mtr...@mindspring.com

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Jun 5, 2019, 10:21:24 AM6/5/19
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Tried this with version 2.4.10:

[rosema1@demeter ~]$ cat /SD5/people/rosema1/L5-50-igv_session_file.xml
<?xml version="1.0" encoding="UTF-8"?>
<Global> genome="http://demeter/SD5/people/rosema1/OsXa13WT" locus="OsXa13WT" version="3"
<Resources>
</Resources>
</Global>

Got:

igv_error.PNG

James Robinson

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Jun 5, 2019, 1:12:27 PM6/5/19
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Sorry but I can't support old releases.

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Mark Rose

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Jun 5, 2019, 1:36:58 PM6/5/19
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I installed the latest version (2.5.3) and it does exactly the same thing
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James Robinson

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Jun 5, 2019, 2:10:58 PM6/5/19
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Well I don't know where to go with this since I can't reproduce it.    Perhaps you could be more precise than "it doesn't work",  the screenshot you show indicates that the genome or fasta file was successfully loaded, but the bam file you loaded does not have any sequences with names matching the sequences in the fasta file.    That is a different problem unrelated to sessions and web links.

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Mark Rose

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Jun 5, 2019, 2:32:10 PM6/5/19
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Genome "A" was the genome that was loaded when I opened IGV.  When I loaded the session file with


it is specifying the use of OsXa13WT instead, which it does not load as supposedly it should, hence the error.

[rosema1@demeter ~]$ cat /SD5/people/rosema1/L5-50-igv_session_file.xml
<?xml version="1.0" encoding="UTF-8"?>
<Global> genome="http://demeter/SD5/people/rosema1/OsXa13WT" locus="OsXa13WT" version="3"
<Resources>
<Resource name="L5-50 align" path="http://demeter/SD5/people/rosema1/L5-50-vs-OsXa13WT.fa.sort.bam"/>
</Resources>
</Global>

[rosema1@demeter test1]$ samtools view -O SAM /SD5/people/rosema1/L5-50-vs-OsXa13WT.fa.sort.bam
L5-50_0.24259-SR_R18.5785824.B190515_C1475.ab1  CHROMAT_FILE: L5-50_0.24259-SR_R18.5785824.B190515_C1475.ab1 PHD_FILE: L5-50_0.24259-SR_R18.5785824.B190515_C1475.ab1.phd.1 CHEM: term DYE: big TIME: Wed May 22 15:55:01 2019        0       OsXa13WT        375     46      113=10D361=     *       0       0       TAGCTAGAGAGGAAGGCTTAAGTGCTACTACAACTGCATGTGTGGTTTGGCCTTGGCCATGGCTCAGTGTTTATATAGTTGGAGACCCTCCACTTTTGGTGGTGTACAGTAGGTATCTAACCTTTGTTTTTTTTTTCTTGTGCTTGATATTTCTTTTTCACTCTGATATATCATTTATATGAATTTTCTTTTTCTACCTCTAGATCTGTCCCTCTCTCCACTACTCTGAATATGTGGTCATATGAATGCATAACTGAGGGGCAATATGACACGTATGACCACTCAGTGTGTCTGTTGCCATTTGGAGAGCTGGAGCTCTCATATAGGTTTCTTTTACTTGTTACAATAGTTGAAATGTTATTGAAAATTTTCTTGATTTGTGTAGTTTTATTTGTAGAAGGATGTACAACCATGGACAATGATGCAACTTAATTAGTAACATGTTGGGTGATCCATCAATCGACTTCTATCGTC        *       NM:i:10 AM:i:46

James Robinson

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Jun 5, 2019, 2:37:57 PM6/5/19
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Ah, yes, understood.  But I again I have tested this exact case with my own files, and a number of other variations on this as well.   So I don't really know what else to do.    I assume when you have tried entering "http://demeter/SD5/people/rosema1/OsXa13WT" in a web browser and confirmed that your fasta file is loaded.  Its unusual to see a fasta file without an extension but legal.

If you can attach your igv.log file I'll look for errors there.   First shutdown igv and delete or rename it, then start and produce the error, shutdown and send the file.  The igv.log file is in  "<user home>/igv"
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