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Are these excluded from Tophat if they are from diffferent chromosomes?
Any suggestions on packages that can do this determination?
Any suggestions on packages that can do this determination?
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I donot think so....but there are some packages for DNA fusion/translocation detection.. -
townway, could you point to dna fusion packages? I know pemer is a good one for translocation detection, but probably not for rna-seq data--
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right now there are some for DNA, like pemer, breakdancer. and I have not seen one for rna-seq. if you know, please post me as wellComment
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I think for tophat, it does not report fusion transcript from different chromosomeComment
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Including TopHat there are many more tools which can detect fusions both within and between chromosomes.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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