View Single Post
Old 05-09-2013, 06:53 AM   #1
zshuhua
Junior Member
 
Location: Ontario

Join Date: May 2010
Posts: 4
Default FastQC: odd kmer content

Hi,
I'm checking the data quality using fastqc for the Illumina Hi-Seq2000 reads and got odd kmer patterns (see attachment). Although an old thread suggested that 5' pattern is common, I want to know how to eliminate the odd patterns for GGGGG, AAAAA and TCTTC. Could you please help to interpret and get rid of them?
Thanks in advance!
Attached Images
File Type: png kmer_profiles.png (78.8 KB, 108 views)
zshuhua is offline   Reply With Quote