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What is your recommendation for analyzing bisulphit data? There are very few tools with various output (generally non human readable) and performance (Socs-B, Bathmeth, Bsolana, Pass) but I think we don't find the real one, yet.
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Bisulfite sequencing and solid is a very very very very very very very very very very very very very bad idea. -
13 very's seems a little harsh, but I agree with the sentiment. If you have any kind of choice then using colourspace for BS-Seq is best avoided. The techniques used for mapping of BS-Seq data in base space don't naturally extend to colorspace so you have to make somewhat uncomfortable compromises about how to do the analysis.
Having said that, if you have to go ahead with this then we'd probably recommend BSolana. We talked a lot with the authors when they were writing it and they were well aware of the limitations of the platform and made a reasonable compromise to get the best they could out of this type of data. It might be worth noting that they moved to Illumina sequencing not long after writing Bsolana though!Comment
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I agree with you, B-Solana is a good compromise but unfortunately we have some program errors with this on the latest linuxes. I'll set up a VM with an older version of Ubuntu/CentOS etc. and give it a last try.Originally posted by simonandrews View PostComment
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Have you tried contacting the authors? They're nice guys and may be able to offer a quick fix. If it worked on older linux versions it's probably a really trivial fix.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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