Does someone know which tool can detect fusion gene form Solid single end 50bp reads. I found several softwares such as FusionMap,FusionSeq and so on. But some need paired end reads and some cant't handle colorspace reads. Now I still didn't find a tool to do the job with my data. Can someone help me. Thank you very much!
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I made a number of Whole Transcriptome Analyses with SOLiD 50bp fragments and fusion detection with Lifescope WTA pipeline. It does work quite well, although I would agree that there will be false positives with fragments - but the number of supporting reads for each fusion will be there to help you and screen these cases. It also will give you files for circos visualization, that will even work with a minimal tweaking ..
HTH
Alessandro
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