I aligned my PE sequencing data with TopHat. Now I'm trying to find a way to extract fusion transcripts (where wither a junction exists >1Mb or on a different chromsome). Is it possible to extract this from the SAM file, or is it automatically not mapped by TopHat?
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I dont think you can. you can try "hydra-sv" http://code.google.com/p/hydra-sv/#S...in_Hydra_suite -
Even I am having the same question, to find fusions can we find unmapped reads from the SAM file generated by tophat2 without fusion search OR we should go for whole fastq file with fusion search option of tophat2 ?
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