Question: Fastqc Shows A Weird Kmer Distribution
0
gravatar for Nick
5.9 years ago by
Nick260
Spain
Nick260 wrote:

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

kmer distribution

kmer distribution

enter image description here

illumina fastqc • 2.4k views
ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Nick260
3
gravatar for kelvin.c.chan
5.9 years ago by
kelvin.c.chan30 wrote:

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

ADD COMMENTlink written 5.9 years ago by kelvin.c.chan30

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

ADD REPLYlink written 5.9 years ago by Nick260
0
gravatar for Nick
5.9 years ago by
Nick260
Spain
Nick260 wrote:

@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

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Nick260

How did you remove the TruSeq-containing sequences?

ADD REPLYlink written 5.9 years ago by bow790
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 709 users visited in the last hour