Reduced representation bisulphite sequenceing with Solid

HelenM · 06-27-2012, 04:30 PM

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!

PeteH · 06-27-2012, 05:09 PM

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

HelenM · 07-03-2012, 09:50 PM

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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06-27-2012, 04:30 PM	#1
HelenM Junior Member Location: New Zealand Join Date: Nov 2011 Posts: 4	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!

06-27-2012, 05:09 PM	#2
PeteH Member Location: Melbourne Join Date: Jun 2010 Posts: 43	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

07-03-2012, 09:50 PM	#3
HelenM Junior Member Location: New Zealand Join Date: Nov 2011 Posts: 4	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.