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Old 09-16-2011, 12:09 PM   #1
mattanswers
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Location: Boston

Join Date: Oct 2009
Posts: 65
Default interpretation of FASTQC Overrepresented Kmers

I am analyzing our results of 91 base single end Illumina sequencing with FASTQC and have attached two .png images, one of the graph and the other of the graph and list of kmers. The sample, part of a ChIP-Seq experiment, is 'input' DNA.

I have a couple of questions with regard to interpretation.

First, a large portion of the listed kmers are part of the adaptor:
GATCGGAAGAGCTCGTATG. All kmers in postions 1-9 are part of the adaptor, but only the first 13 bases of the adaptor. Kmers covering bases 14-19 of the adaptor are listed, but their positions are listed as 85-86 ! It seems like sequences were inserted inside the adaptor ? Does anyone have an explanation for this ?

Second, in the graph of relative enrichment vs position in read, there is gradual rise in the 6 listed kmers from positions 30-34 to about position 70 or so. Because 5 of these 6 kmers included in the graph are part of the adaptor, as can discerned from the leftmost part of the graph in postions 1-5, what does it mean that the relative enrichment of these kmers rises from position 30 to position 70 ?
Attached Images
File Type: png Kmer_graph.png (36.7 KB, 136 views)
File Type: png Kmer_content.png (82.6 KB, 154 views)
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