Question

Fastqc Shows A Weird Kmer Distribution

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10.8 years ago

Nick ▴ 290

I ran FatsQC on a set of 4 Illumina PE exomes and got really weird graphs for the kmer distribution. I've never seen this pattern before - does anyone know what is going on and what to do about it?

kmer distribution

enter image description here

illumina fastqc • 3.6k views

ADD COMMENT • link 10.8 years ago by Nick ▴ 290

score 3 · Answer 1 · 2013-07-12

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10.8 years ago

kelvin.c.chan ▴ 30

Those k-mers almost perfectly correspond to the TruSeq adapter sequence. Was there anything peculiar that showed up in the overrepresented sequences table?

ADD COMMENT • link 10.8 years ago by kelvin.c.chan ▴ 30

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You are right - there are TruSeq adaptors among the overrepresented sequences. I'll remove them and then re-run fastqc.

ADD REPLY • link 10.8 years ago by Nick ▴ 290

score 0 · Answer 2 · 2013-07-14

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10.8 years ago

Nick ▴ 290

@kelvin.c.chan: I did remove the over-represented sequences for one of the samples and the graph changed somewhat but there are still peaks (see below) although fastqc no longer reports any over-represented sequences. Any ideas? kmer distribution