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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 ?
pls guide asap.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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