Zoomable Plot Tool For Copy Number Data And Snp Data

Question

[dan.brewer]

Does anyone know of any plotting software that will allow you to interactively zoom into regions of a scatter plot?

We have two csv files that have been generated from Illumina NGS data:

1. binned copy number (chromosome, position, total read depth)
2. SNP allelic ratio (chromosome, position, allelic ratio)

We would like to be able to explore this dataset, zooming into specific regions and looking at the finer details. If possible it would be great to be able to select chromosome, show both datasets at once, and if you zoom in on one dataset it will also zoom in on the other.

Any ideas?

[Zev.Kronenberg]

have you tried IGV?

[Irsan]

Like Zev said, try IGV. You might want to convert your binned copy numbers to copy number format of IGV (http://www.broadinstitute.org/software/igv/CN) and the SNP allelic ratio to LOH-format (http://www.broadinstitute.org/software/igv/LOH) and if you have done segmentation on your copy numbers try the segmentation format (http://www.broadinstitute.org/software/igv/SEG).

Answer 1

[Julien Textoris]

Hi,

I remember I used a tool called XMAPCORE. I used it with exonArray transcriptional data, and it allowed to make quite easily various plot on a zommable genome. The doc is well written. If i find the script where I used it, i'll paste it here.

Julien