I have small DNA fragments (avg 44 nt) that I would like to sequence but this is out of the recommended range of the GAII. I understand the limits of larger fragments (limited cluster density/large clusters) but, aside from the physical limitation of forming the bridge, what is the real limit to smaller insertions? I have circularized padlock probes from as short at 90 bps meaning the oligo must for a complete circle rather then just a 180° bridge, so the pliability of DNA shouldn't really be a factor.
Has anyone sequences this small of a fragment and if so, what were the limits and what recommendations do you have?
For technical info there will only be ~20 - 30 unique sequences so I anticipate 10K coverage, so if cluster formation efficiency is the issue for smaller fragments, I should still have more than enough coverage.
Has anyone sequences this small of a fragment and if so, what were the limits and what recommendations do you have?
For technical info there will only be ~20 - 30 unique sequences so I anticipate 10K coverage, so if cluster formation efficiency is the issue for smaller fragments, I should still have more than enough coverage.
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