I follow Peterson et. al 2012's procedure for ddRAD-Seq. I ran PCR products-only and SPRI cleaned PCR products on a fragment analyzer, and seems like my PCR products are pretty clean and they are at the desired fragment range.
My problem is losing too much DNA when I clean-up PCR products with SPRI.
Do you think I can directly send my PCR products to Illumina sequencing?
I think it's possible. I don't see anything wrong with that
normally it is required to clean the products that you eliminate anything which can interfere in sequencing. One can actually send the pCR product directly also.
I use AMPure beads to clean up my ddRAD libraries after PCR, they sequence great and still keep a large amount of product.
it is better to to clean the products. In my experience there are many primer dimers in the pcr products which will affect number of useful reads.
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