prediction-free differential exon-usage analysis

[frymor]

Hi all,

I have a RNAseq data set from the drosophila genome without replica. I would like to run a differential exon-usage analysis on this data set.

The genes we are interested in are poorly annotated, so I am looking for a tool which can work without relying on predicted transcripts.

I have found out the cufflink-cuffdiff package can work without replica and run the analysis without relying only on the gtf file, but I would like to know if there are other tools out there who can do the same analysis, but on a friendlier way.

thanks
Assa

PS
I have posted a similar question on biostar, but I hope to get here different responses.

[Brian Bushnell]

I don't know of a better analysis package, but BBMap is good for unbiased RNA-seq mapping that does not rely on existing gene annotations.

[frymor]

thanks for the reply