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Old 06-27-2012, 05:30 PM   #1
HelenM
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Default Reduced representation bisulphite sequenceing with Solid

Hi all,

I was wondering if anyone has had any experience with using the Solid platform for sequencing of RRBS libraries. I can't find any literature on this, everyone seems to use Illumina.

I suspect it may be problematic, but we have a Solid sequencer our lab so it would be great to find a protocol for using it with RRBS.



Cheers!
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Old 06-27-2012, 06:09 PM   #2
PeteH
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I'm not sure if this is much help, but this paper used SOLiD to do whole-genome BS-seq http://www.ncbi.nlm.nih.gov/pubmed/21706001. One of the difficulties you'll face will be in aligning BS-converted SOLiD data since most BS-aligners focus on base-space reads (e.g. Illumina). Ben Langmead (one of the authors of the linked paper) has a program to align SOLiD BS-data (albeit whole-genome), but my understanding is that the program is still in beta.
Pete
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Old 07-03-2012, 10:50 PM   #3
HelenM
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Thanks very much Pete. We have just decided to go for Illumina instead for our RRBS work, so thankfully I no longer have to worry about this.
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