SOLiD unmapped RNA-seq reads from TOPHAT

[rkk]

Hello,

I am working on SOLiD RNA-seq data. I would like to find chimeric transcripts or fusion genes discovery with this data. But, the softwares, which does fusion genes discovery were written for FASTQ format files.

So, I tried converting my color space files to fastq by solid2fastq in BFAST and MAQ and the fusion genes discovery with the resulting files was a disaster as the conversion of .csfasta files to FASTQ is not straightforward as described in BFAST and MAQ

I thought I can convert the mapped colorspace reads to FASTQ files and use those softwares.

Is there a way to get the mapped reads and unmapped reads from TOPHAT? or any other alternatives to solve my problem?

Any help in this regard will be greatly appreciated.

Thanks,

[colindaven]

A nice alternative might be to do mapping with eg bioscope in colourspace and then read the BAM files into R using a package like edgeR.

I mention edgeR since they wrote a very nice step by step pdf, available on this forum, which could get you started.