RNAseq analysis SOLiD

[Raa]

I am going to sequence two different subtypes of tumors using paireend chemistry on SOLiD. My aim is to study differential expression, alternative isoforms, fusion genes and long non coding RNAs.
I want to know what tools are best suited to analyse all the above (eg. mapping tools, tools to find fusion genes etc.). I an not interested in using bioscope/lifescope.
I would be happy if any of the members able to give information about the sources where RNAseq analysis was explained in a way understandable to the naive'

[colindaven]

I would suggest NovoalignCS as a capable mapper, then SAM>BAM conversion and use of the edgeR pipeline for differential expression.

I haven't looked into fusion gene detection for SOLiD data, and think you might struggle a bit here to find software.

[Krish_143]

You can also try Tophat-cufflinks-cuffdiff-cummeRbund.

[mbblack]

To be honest, I think you will get your best color space mapping using LifeScope - their mapping algorithm seems to do very well.

You can always do your desired downstream analysis with any tool you want, but for actually mapping, I don't think you will get better results than with LifeScope (not mapping in color space anyway).