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07-23-2013, 03:23 AM
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#1 |
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Junior Member
Location: South Africa Join Date: Jul 2013
Posts: 5
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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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07-23-2013, 03:49 AM
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#2 |
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Senior Member
Location: uk Join Date: Mar 2009
Posts: 667
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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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07-29-2013, 02:04 AM
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#3 |
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Junior Member
Location: South Africa Join Date: Jul 2013
Posts: 5
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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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07-29-2013, 02:24 AM
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#4 |
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Senior Member
Location: uk Join Date: Mar 2009
Posts: 667
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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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| fastqc, kmer |
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