Making nice image of chr1 coverage track in IGV

[sindrle]

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...

[dpryan]

Have a look at the Gviz bioconductor package, it can create images like that.

[sindrle]

Looks nice! I guess I just have to start trying.

Thanks!

[sindrle]

Just realised mouse don't have centromeres..

Any good ideas how to make a similar image for mouse? Thanks!

[frozenlyse]

That just looks like custom data loaded to UCSC?

[emp]

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...

[frozenlyse]

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

[sindrle]

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!

[dpryan]

Never discount the utility of Photoshop/Illustrator when making figures