How Could I Display Two Connected Exons Of Different Chromosomes In Ucsc Browser

Question

[biorepine]

Hi, biostars,

How could I display two connected exons of different chromosomes in UCSC browser. Thanx in advance.

ex:

chr10    100034651    100034652    exon1_chr10    0    -    chr5    130267883    130267884    exon1_chr5    0    +

[Aaronquinlan]

That looks like our BEDPE format that we defined for HYDRA. If you find a way to do this, I'd love to know.

[biorepine]

Is the same format we use for long-range chromatin interaction maps (5C/ChIA-pET). I wrote a small script that converts BEDPE into BED12. However this only works if the 2 chromosomes are similar.

Answer 1

[Obi Griffith]

There was a related question about how to vizualize fusions with a few solutions suggested (How to visualize gene fusions to better illustrate the gene structure?). I really like the look of the visualizations that these guys present in their paper and the corresponding Genomatix Transcriptome Viewer (TViewer) tool. But, unfortunately it seems this is only a commericial solution requiring you to purchase not only their software system but also their hardware. I'd love to hear suggestions of how others visualize fusions. We still tend to do this manually on a case-by-case basis.