Detection of chimeric reads

[Ijon.Tichi]

Hi all,

What is the best way in terms of time/sensitivity to search for reads from the different parts of the same genome or combined genomes? Specifically, for the short reads and big BAM files.
I know that BWA-SW looks for such reads but it requires long reads. It seems there are plenty of such tools for the RNAseq data. Could you advise the most effective way for the DNAseq paired-end data? Does anybody use chimerascan tool for such purposes?
Thanks!

[JackieBadger]

I have used Uchime (http://www.drive5.com/uchime/) before when studying MHC amplicons. May be applicable

[Ijon.Tichi]

Thank you, JackieBadger. This tool looks promising.

[jp.]

may you tell me how to get exact fusion break-point from chimerascan ? it gives only spanning reads but not the break point seq.
thank you

I have used Uchime (http://www.drive5.com/uchime/) before when studying MHC amplicons. May be applicable