Cannot see the entire genome

[khork...@gmail.com]

Hello,

When I zoom out the genome to the smallest, I cannot see the entire genome coverage. When I zoom in to the middle or higher, part of the genome coverage show up. Can I just see the whole genome without zoom in.

Thanks.

[James Robinson]

Hi, coverage of what?  Are you referring to alignments from a bam file?

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[khork...@gmail.com]

Thanks for your quick response. I partially sequenced multiple isolates of Vibrio cholerae. I want to map the field isolate contigs to reference Vibrio cholerae genome. I imported each set of contigs from multiple SAM files. Now I am looking for the genome region with the largest number of mapped contigs from the isolates. Specifically, I am looking for the region in the reference genome which has the highest coverage with contigs from filed isolates. To identify this region, I need to zoom out to see the entire genome.

Thank you!

Jessica

On Wednesday, April 12, 2017 at 10:11:40 AM UTC-4, Jim Robinson wrote:

Hi, coverage of what?  Are you referring to alignments from a bam file?

On Tue, Apr 11, 2017 at 2:12 PM, <khork...@gmail.com> wrote:

Hello,

When I zoom out the genome to the smallest, I cannot see the entire genome coverage. When I zoom in to the middle or higher, part of the genome coverage show up. Can I just see the whole genome without zoom in.

Thanks.

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[James Robinson]

To see whole genome coverage you will have to precompute it.  You can use igvtools for this, see the "count" command here:  http://software.broadinstitute.org/software/igv/igvtools_gui

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[khork...@gmail.com]

Hello Jim,

Thank you for your answer. Now I can see the whole genome. Is it possible to export the histogram into excel to show the coverage at each position? I am interested in identifying the genome positions with highest coverage. Thanks.

Jessica

On Wednesday, April 12, 2017 at 3:16:56 PM UTC-4, Jim Robinson wrote:

To see whole genome coverage you will have to precompute it.  You can use igvtools for this, see the "count" command here:  http://software.broadinstitute.org/software/igv/igvtools_gui

On Wed, Apr 12, 2017 at 2:24 PM, <khork...@gmail.com> wrote:

Thanks for your quick response. I partially sequenced multiple isolates of Vibrio cholerae. I want to map the field isolate contigs to reference Vibrio cholerae genome. I imported each set of contigs from multiple SAM files. Now I am looking for the genome region with the largest number of mapped contigs from the isolates. Specifically, I am looking for the region in the reference genome which has the highest coverage with contigs from filed isolates. To identify this region, I need to zoom out to see the entire genome.

Thank you!

Jessica


On Wednesday, April 12, 2017 at 10:11:40 AM UTC-4, Jim Robinson wrote:

Hi, coverage of what?  Are you referring to alignments from a bam file?

On Tue, Apr 11, 2017 at 2:12 PM, <khork...@gmail.com> wrote:

Hello,

When I zoom out the genome to the smallest, I cannot see the entire genome coverage. When I zoom in to the middle or higher, part of the genome coverage show up. Can I just see the whole genome without zoom in.

Thanks.

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[James Robinson]

No, not from igv.   I actually think you want to use an analysis tool for that sort of work.   Look at bedtools.

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