11 September 2014

RADseq, Illumina, and fastqc

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RADseq fastqc

Two libraries were sequenced on Illumina HiSeq 1500 in RapidRun mode at VCC.

Lane 1 - RAD4: repeat of Pogonomyrmex RAD-seq

RAD4 fastqc

• no filter applied in bcl2fastq (--with-failed-reads) conversion due to low complexity in restriction site region
• overall read quality looks good

Lane 2 - ddRAD1: first 48 samples of Aphaenogaster double-digest RADseq protocol [1]

ddRAD1 fastqc

• normal filters in bcl2fastq
• read quality crappy
• 10th percentile sequence quality drops from 10.6 to 2 (minimum) at 40 bp while median doesn’t change
• median quality drops from 23 to 4.5 at 85 bp

[1] Peterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S., and Hoekstra, H.E. (2012). Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. PLoS ONE 7, e37135.