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Old 06-10-2015, 08:25 AM   #9
ksawatzki
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Location: Boston

Join Date: Jun 2014
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I haven't taken a detailed look at the fastq since it's a complete loss for us (even though R1 is completely normal, we require both) and also because we're not involved with the sequencers themselves. However, on cursory glance, it looks like the dominant two read types are poly-C runs and N-dominated. Even reads with some nucleotide diversity pretty much are universally 0 scores. The sequences definitely do not make sense and are obviously not biological. Just to clarify, all the R2 reads are the full 300bp long.
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