Fusion or Chimeric gene discovery tools

[Debu_013]

I browsed through a few fusion gene discovery tools like deFuse and SOAPfuse and found that they all have established a pipeline wherein they accept input as fastq and do the alignment with a tools like Bowtie2 or BWA and then do the down stream analysis.

I have already generated alignments- SAM/BAM files using both STAR and Bowtie2.

I wanted to know if there are any tools that I could now use to do downstream analysis of the data to find fusion genes.

[kopi-o]

FusionMap (http://www.omicsoft.com/fusionmap/#[[%283%29%20Options]]) is one program that does allow BAM/SAM input (although I have only used it starting from .fastq myself).

I guess you need to be careful about how you map your FASTQ files initially to make sure that possible fusions are not filtered out. Perhaps that's why most packages do the mapping internally.

[Debu_013]

I guess that is reasonable.
By the way, in your experience which Fusion detection tool would you suggest?

I was thinking of using deFuse or SOAPfuse and Tophat2.

[ndaniel]

Also FusionCatcher is very good and very easy to use! It found plenty of novel fusion genes!

http://code.google.com/p/fusioncatcher/