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Old 04-25-2018, 10:25 AM   #5
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Location: Flagstaff, Arizona, USA

Join Date: Mar 2015
Posts: 5


My in-silico digest (simRAD in R) returned only ~100k fragments that meet a size-selection criteria of ~150-550 bp, which I'll target for my sequencing runs. That criteria is surely why there were only 100k fragments instead of millions.

To answer your question, I do not know of an alternative to using methylated adapters for this kind of work, so that is precisely what I've chosen to use...for now.

I'd like to raise another aspect of my initial question on this thread: I have inexpensive & easy access to a NextSeq500, but have the sense that the HiSeq4000 might be the best platform for my full sequencing effort once this pilot study is complete. Given that the number of reads obtained from one NextSeq500 run (~400M) versus one lane of HiSeq4000 (~300M) are roughly comparable, what other factors should be considered for deciding which platform would be best for a ddRADseq approach?
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