mm10 genome for igvtools

[Tea Berulava]

Could somebody help me with adding mm10 genome to igvtools? I need to obtain tdf files, and the only reference which comes together with igvtools is hg19.

Many thanks in advance and looking forward to your suggestions.

Best

Tea Berulava

[James Robinson]

Actually all supported genomes, including mm10,  are included with the igvtools download.   Could you be more specific about what your issue is?

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[Tea Berulava]

Hi Jim, 

Thank you very much for your reply. here it come what I did:

1. i downloaded igvtools from https://software.broadinstitute.org/software/igv/download

2. I unzipped and installed it from terminal

3. igvtools folder was created on my computer with hg refgenome only (see attaced file).

4 when i tried to create tdf file with following command "igvtools count -z 5 -w 10 -e 0 examplefile.bam examplefile.tdf mm10" in terminal I got message "Genome definition file not found for mm10" (see attached file)

I attached screenshots that you see directly what I mean.

Thank you very much and looking forward to hearing from you.

best, 

tea

On Wednesday, January 18, 2017 at 7:36:56 PM UTC+1, Jim Robinson wrote:

Actually all supported genomes, including mm10,  are included with the igvtools download.   Could you be more specific about what your issue is?

On Wed, Jan 18, 2017 at 8:50 AM, Tea Berulava <tea.be...@gmail.com> wrote:

Could somebody help me with adding mm10 genome to igvtools? I need to obtain tdf files, and the only reference which comes together with igvtools is hg19.

Many thanks in advance and looking forward to your suggestions.

Best

Tea Berulava

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To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

[Helga Thorvaldsdottir]

Hi tea,

Your screenshot of the finder showing the genomes directory seems to be of your main igv directory, not the IGVTools directory. I just tried downloading igvtools from https://software.broadinstitute.org/software/igv/download and the info required for mm10 was there. Did you move the igvtools.jar to the main igv directory and run it from there? If so, it is trying to pick up the genome from the igv/genomes directory, not from the IGVTools/genomes directory. The igv/genomes directory will not necessarily have all the genomes, as its contents depend on which genomes you have used with the IGV desktop application.

Helga

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/7caa8924-a306-495b-a83a-928debabef97%40googlegroups.com.