ddRAD protocol by Peterson et al.
Hi,
Our lab really enjoyed reading Peterson et al. article in PLOS on ddRAD and we have plans to their protocol. I have some question at this stage and I'm wondering if someone please can answer?
1.Have you ever tried to sequence the ddRAD libraries on MiSeq? We would like to do this but the Norwegian Sequencing Center (http://www.sequencing.uio.no/) informed us that monochromatic motives (ie AATTC entire flow cell because of the EcoR1 digestion) can be difficult to handle for the MiSeq., so if this is the case, there will have to be adjusted slightly in the run parameters, so the failure to detect this motif (AATTC). However, get round this by blending the library with PhIX to 50% (!), and lowering the clustering density to 50% of normal. The result of course is that we only get 25% of the possible output of the MiSeq…
2. How much PhiX did you load?
Best,
Hanne
Our lab really enjoyed reading Peterson et al. article in PLOS on ddRAD and we have plans to their protocol. I have some question at this stage and I'm wondering if someone please can answer?
1.Have you ever tried to sequence the ddRAD libraries on MiSeq? We would like to do this but the Norwegian Sequencing Center (http://www.sequencing.uio.no/) informed us that monochromatic motives (ie AATTC entire flow cell because of the EcoR1 digestion) can be difficult to handle for the MiSeq., so if this is the case, there will have to be adjusted slightly in the run parameters, so the failure to detect this motif (AATTC). However, get round this by blending the library with PhIX to 50% (!), and lowering the clustering density to 50% of normal. The result of course is that we only get 25% of the possible output of the MiSeq…
2. How much PhiX did you load?
Best,
Hanne
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