Visualization Split Reads mapped with Segemehl

Question

[daron.6]

Hello,

I am working with split read to analyze structural variant and circular DNA. I find that the tools Segemehl in extremely efficient to map split reads.

However, my question is do someone find a way to visualized in a browser the split reads map using Segemehl?

For instance, I am using IGV, that is working great to visualize the read, but I could not find a way to visualize the junction between a split read, as they say it is possible in the manual to do using TopHat.

It look like IGV can only work with splicing read that have a gene structure: "Furthermore, the aligner must assign reads XS tag values. For example, XS:A:+ for GT-AG intron boundaries and XS:A:- for CT-AC intron boundaries."

Answer 1

[David Langenberger]

Check this post: running segemehl problem

By using testrealign.x with the -n option, you get a BED file with the junctions. These junctions can be loaded to IGV. But, of course, you can only visualize normal, circular and strandswitch junctions. Junctions from fusion genes (e.g. on two different chromosomes) can not be visualized using BED files and IGV.