Chimerascan Rna-Seq Fusion Tool

Question

[learnerforever]

We recently ran chimerascan successfully and got the fusion candidates in the bedpe format as specified on http://code.google.com/p/chimerascan/wiki/Running

Is there a way to "visualize" the fusions using IGV or other viewer? It seems that the program generate several BAM files but I am not sure if any of those contain discordant reads aligned in such a way that IGV can show them with different colors etc.

Any help in visualizing candidate fusions from ChimeraScan would be appreciated.

Thanks forum.

Answer 1

[Malachi Griffith]

For visualizing the underlying reads that support a chimeric transcript you might try the genome browser: Savant

Or tools like: Pairoscope or possibly even Circos, or Hive plots perhaps. For pure flexibility you might try generating custom visualizations in R as well.

Answer 2

[mht]

I've been running ChimeraScan and would like to also view reads supporting each fusion gene candidate on some kind of viewer. I've been trying IGV and Savant, but my problem is, I'm not sure which BAM file I'm supposed to be using. Some help in this area is very much appreciated. Thanks!