Help with FastQC interpretation

ronton · 08-13-2014, 03:07 PM

I am wondering if anyone can help provide possible explanations for my FastQC results, specifically the red Xs for Adapter Content and Kmer Content. These were .fastq.gz files straight from an Illumina HiSeq 2500, 100bp paired end reads. 'Casava FastQ Files' filter was used to group multiple files for the single sample.

Under Adapter Content, the Illumina Universal Adapter line comes up around 42bp with a value of 10% at 84bp. For Kmer Content, the curves begin at 73bp and reach a value of 6 by 90bp.

Is this bad? Should I trim adapters for example with BBDuk and run FastQC again? Any help is appreciated, thank you.

nucacidhunter · 08-13-2014, 03:22 PM

This is not bad. Both of those indicators are most likely result of sequencing library fragments with inserts shorter than 100 bp, so part of adapters also have been sequenced. I would suspect that qualitry scores also dropping toward ends more than usuall. Trimming adpters should fix both issues.

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08-13-2014, 03:22 PM	#2
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,248	This is not bad. Both of those indicators are most likely result of sequencing library fragments with inserts shorter than 100 bp, so part of adapters also have been sequenced. I would suspect that qualitry scores also dropping toward ends more than usuall. Trimming adpters should fix both issues.