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Old 01-07-2012, 08:52 AM   #1
brachysclereid
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Location: California

Join Date: Feb 2011
Posts: 32
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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