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Old 07-23-2013, 03:23 AM   #1
Potjie
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Default FastQC GGGGG Kmer

Hi all,

I sequenced a genome on the Illumina MiSeq using paired ends. When analyzing the second read in FastQC, there is a steady increase of a over represented kmer (GGGGG).

Does anyone know what would cause this effect and whether it is indicative of an underlying problem?
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Old 07-23-2013, 03:49 AM   #2
mastal
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I have sometimes seen stretches of poly G (as well as poly A) when the inserts are very short and you read into the Illumina adapters, and then past the end of the adapters.

Does the GGGGG kmer remain if you quality trim your reads and remove adapters?
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Old 07-29-2013, 02:04 AM   #3
Potjie
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The GGGGG kmer does disappear after trimming.

I just wondered what could be the cause of such a artifact. Thanks
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Old 07-29-2013, 02:24 AM   #4
mastal
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Default FastQC GGGGG Kmer

once you get past the end of the adapters, it is either complete rubbish, or the sequences on the flow cell.
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