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Old 01-13-2016, 04:03 AM   #3
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Location: uk

Join Date: Mar 2009
Posts: 667

Are all the reads in the R1 and R2 files the same length?

I think sometimes if the reads have been trimmed to remove low quality bases, symbols representing low values will be missing, and the file may look like one from a different quality encoding.

Have you run the file through FastQC, and is it FastQC that has decided the R1 and R2 files have different quality encoding?
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