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Old 09-20-2011, 12:40 PM   #2
Yilong Li
Location: WTSI

Join Date: Dec 2010
Posts: 41


we've seen a similar rise of adaptor kmers towards the ends of the sequences. We haven't done anything formal analysis, but since we got paired-end sequences, we've been able to align the paired reads together, and it seems that many reads having adapter kmers originate from DNA fragments that are shorter than the read length. When this happens, sequencing will first proceed through your original DNA fragment and then continue to sequence the adapter sequence located immediately after it.

We have also seen weird patterns in nucleotide distributions in <8 bps of the 5'-end of the reads, but have no idea where it comes from. If you find out let me know.
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