kmer content in the first bases of Illumina sequence

brachysclereid · 01-07-2012, 09:52 AM

I have seen odd kmer content in the first bases of Illumina reads in my data and others. Does anyone have an idea about why this is? The barcodes were trimmed already by the Cassava pipeline. Here are some examples that I found on the web for different species:

http://genomevolution.org/wiki/index...rst_Run_FastQC

http://www.msi.umn.edu/~ztu/RNAseq/fastqc_report.html

https://notendur.hi.is/haj16/fastqc_report.html

simonandrews · 01-09-2012, 01:26 AM

These sorts of pattern are pretty common (almost to the point of being universal) in RNA-Seq libraries. Apparently it's the 'random' hexamer priming which isn't as random as you might hope.

PeteH · 01-09-2012, 03:54 PM

Quote:

Originally Posted by simonandrews

These sorts of pattern are pretty common (almost to the point of being universal) in RNA-Seq libraries. Apparently it's the 'random' hexamer priming which isn't as random as you might hope.

I think Simon may be referring to this paper:
Hansen, K.D., Brenner, S.E. & Dudoit, S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38, e131–e131 (2010) (http://www.ncbi.nlm.nih.gov/pubmed/20395217)

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01-07-2012, 09:52 AM	#1
brachysclereid Member Location: California Join Date: Feb 2011 Posts: 32	kmer content in the first bases of Illumina sequence I have seen odd kmer content in the first bases of Illumina reads in my data and others. Does anyone have an idea about why this is? The barcodes were trimmed already by the Cassava pipeline. Here are some examples that I found on the web for different species: http://genomevolution.org/wiki/index...rst_Run_FastQC http://www.msi.umn.edu/~ztu/RNAseq/fastqc_report.html https://notendur.hi.is/haj16/fastqc_report.html

01-09-2012, 01:26 AM	#2
simonandrews Simon Andrews Location: Babraham Inst, Cambridge, UK Join Date: May 2009 Posts: 871	These sorts of pattern are pretty common (almost to the point of being universal) in RNA-Seq libraries. Apparently it's the 'random' hexamer priming which isn't as random as you might hope.