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Old 03-04-2014, 06:26 AM   #1
sindrle
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Default Making nice image of chr1 coverage track in IGV

Can anyone help me make this kind of image?

I have calculated the coverage track and visualised (as log values) compared to chr1 in IGV.

However in IGV i can't see the centromere, nor the whole chromosome, so the image is not as nice as this one...


Screen Shot 2014-03-04 at 16.20.35.jpg
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Old 03-04-2014, 06:44 AM   #2
dpryan
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Have a look at the Gviz bioconductor package, it can create images like that.
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Old 03-04-2014, 07:30 AM   #3
sindrle
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Looks nice! I guess I just have to start trying.

Thanks!
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Old 03-04-2014, 11:56 AM   #4
sindrle
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Just realised mouse don't have centromeres..

Any good ideas how to make a similar image for mouse? Thanks!
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Old 03-04-2014, 04:26 PM   #5
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That just looks like custom data loaded to UCSC?
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Old 03-05-2014, 08:53 PM   #6
emp
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Hello,
I want to visualise my mapped SAM file, as to how much of its part contains centromeric region.

Kindly help me as to what tool should be used.

Waiting for help...
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Old 03-05-2014, 09:27 PM   #7
frozenlyse
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Quote:
Originally Posted by emp View Post
Hello,
I want to visualise my mapped SAM file, as to how much of its part contains centromeric region.

Kindly help me as to what tool should be used.

Waiting for help...
convert your sam to bam and then index using samtools, load into IGV
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Old 03-18-2014, 04:26 AM   #8
sindrle
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This what I did:

used Igvtools count on every BAM in the experiment (took 2 days to calculate).

Imported thes TDF into IGV along with correct genome.

Saved chr1 as vector picture.

Opened in Photoshop and moved the coverage track above the chromosome.

Looks nice!
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Old 03-18-2014, 04:29 AM   #9
dpryan
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Never discount the utility of Photoshop/Illustrator when making figures
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