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Old 11-30-2011, 09:01 AM   #1
Location: ma

Join Date: Mar 2011
Posts: 46
Default questions of illumina pe reads fastqc results

We have a set of illumina paired-end RNA seq 50 bp data. The plot of per base sequnece quality is fine (I think), but the plot of Kmer Content looks very weird. I want to have some suggestions about what is wrong in this data. Does it suggest there is an adaptor contamination? Will trimming adaptors help? How should I find the sequence of these adaptors?

Thanks a lot.
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arrchi is offline   Reply With Quote
Old 12-01-2011, 04:07 PM   #2
Location: Boston

Join Date: Oct 2009
Posts: 65

The pink peak is CGTCT and the red is GTCTG, so I would guess you have the sequence CGTCTG in positions 15-20. Likewise, the it seems like the sequence, TATCTCGTATG in positions 38-48.

Somewhere on the SeqAnswers site has been posted Illumina paired end adaptors.

I found CGTCT in a few 5' Illumina adaptors, however, the CGTCT in the adaptors is always followed by a T and not a G.

Also, TCTCG is found in a couple of 3' Illumina adaptors, but it is followed by AGCATAC. So, I am not sure as to what the peaks you have are showing, and the adaptor sequences I have come from 2008.
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