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Old 01-07-2012, 08:52 AM   #1
brachysclereid
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Default 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
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Old 01-09-2012, 12:26 AM   #2
simonandrews
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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.
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Old 01-09-2012, 02:54 PM   #3
PeteH
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Quote:
Originally Posted by simonandrews View Post
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, e131e131 (2010) (http://www.ncbi.nlm.nih.gov/pubmed/20395217)
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