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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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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:
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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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