Go Back   SEQanswers > Bioinformatics > Bioinformatics
Similar Threads
Thread Thread Starter Forum Replies Last Post
Overrepresented kmers at the start of reads kentk Bioinformatics 20 07-23-2014 01:23 AM
FastQC; overrepresented sequences versus a grep mgg Bioinformatics 16 12-23-2011 01:51 AM
fastqc - overrepresented sequences PFS Bioinformatics 3 07-05-2011 06:18 PM
Help interpretation indel labmtl Illumina/Solexa 0 03-29-2011 07:01 AM
splitting 454 reads into kmers for diff expression Jeremy RNA Sequencing 0 01-18-2011 06:17 PM

Thread Tools
Old 09-16-2011, 12:09 PM   #1
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)
mattanswers is offline   Reply With Quote
Old 09-20-2011, 12:40 PM   #2
Yilong Li
Location: WTSI

Join Date: Dec 2010
Posts: 41


we've seen a similar rise of adaptor kmers towards the ends of the sequences. We haven't done anything formal analysis, but since we got paired-end sequences, we've been able to align the paired reads together, and it seems that many reads having adapter kmers originate from DNA fragments that are shorter than the read length. When this happens, sequencing will first proceed through your original DNA fragment and then continue to sequence the adapter sequence located immediately after it.

We have also seen weird patterns in nucleotide distributions in <8 bps of the 5'-end of the reads, but have no idea where it comes from. If you find out let me know.
Yilong Li is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:10 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO