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Old 06-04-2014, 07:48 AM   #4
Corydoras
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Location: Norwich

Join Date: Jan 2014
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Just in case anybody ever has a similar problem or is confused and stumbles across my post:

Looking closer at my files and where the reverse adapter contamination occurred, it became obvious that the rc sequences were actually simply adapter read through and everything that followed was nonesense which Trimmomatic then perfectly removed. This means in roughly 3% of cases, my fragments were too short for the 150bp HiSeq and the RAD size selection did not work perfectly, but considering it is only 3% and it was my first set of libraries I am fairly happy with that.

Above I stated that I was concerned the forward read would not match the reverse read. Now I believe this is only the case in a couple of hundred fragments at best, that do consist of tiny fragments with adapter ligating to other tiny fragments of adapter. The majority of the contamination however presents itself in reverse complementary form.

This all obviously rests upon the assumption that when read-through occurs, it will be reverse complementary of the P2 adapters in the forward reads, and reverse complementary of the P1 adapters in the reverse reads. Please feel free to point out if there is something wrong with my logic!
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