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Old 11-02-2015, 01:51 PM   #4
kerplunk412
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Location: Bioo Scientific, Austin, TX, USA

Join Date: Jun 2012
Posts: 119
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The general idea sounds good to me but I do have some questions/suggestions:

How small is "smallish" for the genome? I guess you have probably already done the math but it is surprising how few reads are actually needed for reasonable coverage of a small genome.

Do you expect methylation to mainly be at CpGs? I believe the idea of RRBS is that digestion by MspI enriches CpGs. Any reason to deviate from this approach for your experiments?

If the genome you are working with hasn't already been sequenced it may be good to sequence one or a few individuals first so you can create an in-silico map of your digestion, which may help you choose enzymes that will best achieve the desired coverage.

You can buy a kit to create your libraries. The company I work for, Bioo Scientific, sells one, and I believe Illumina and one or two other companies have kits as well.

Edit: I realize my last statement could have been clearer. I meant that you can buy a kit specifically for bisulfite-seq library prep. Feel free to PM me for more information.

Last edited by kerplunk412; 11-03-2015 at 02:54 PM.
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