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Old 11-20-2013, 12:26 AM   #1
Blaize
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Default Colorspace bis-seq data analysis on Solid

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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Old 11-20-2013, 06:31 PM   #2
frozenlyse
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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.
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Old 11-20-2013, 11:44 PM   #3
simonandrews
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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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Old 11-26-2013, 12:34 AM   #4
Blaize
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Quote:
Originally Posted by simonandrews View Post
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!
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.
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Old 11-26-2013, 12:36 AM   #5
simonandrews
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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.
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