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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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!
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Originally posted by simonandrews View Post13 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!
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