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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My data is RNA-seq reads, I forgot to tell this.Hope someone can help me.Thanks. -
Have you tried BioScope and LifeScope? Visit these websites to learn more.
http://solidsoftwaretools.com/gf/project/bioscope
(need to register to see page)
http://solidsoftwaretools.com/gf/project/lifescopeComment
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I tried Bioscope, the ABI company gave the package without the fusion gene dectection package, maybe fusion gene can only be well detected with paired-end reads.Comment
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detect fusion gene from Solid single end 50bp reads( colorspace)
be aware that false positives will be significant problem with single reads. I suggest you to switch to paired end readsComment
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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
AlessandroComment
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