Using bwa for split alignments

[abastkowska]

Hi there,

I have RNA data of a mixture of several organisms including Eukaryotes. I would like to map the sequence to a reference genome (only draft genome available and no cdna) of one Eukaryota. I read that BWA is capable to show split alignment (e.g. for detection of genome rearrangements). Which BWA version and how do I apply BWA to get split alignments, so I could see the intron/exons on my draft genome. I would like to try something else then BLAT.

Cheers,
Alex

[colindaven]

I would look at
- STAR
- GMAP (after de novo assembly of RNA-seq data with trinity)

BWA is great but not really intended for your application