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Old 01-13-2016, 03:20 AM   #1
Location: València, Spain

Join Date: Apr 2009
Posts: 48
Default Quality encoding PE reads

I am just checking the quality of a PE sequencing run. What I found it's a little bit tricky since from a PE reads, R1 seems to use a Phred33 encoding system whereas R2 is using a Phred64. However both reads seem to have been sequenced at once.
Any idea? Do you know that it should considered for further steps like trimming?
Thanks a lot.

This file looks like Sanger/Illumina 1.8+ format.
@HISEQ:157:C6U61ANXX:3:1101:1680:2160 1:N:0:GTCCGCACTCTTTTCC

This file looks like Solexa/Illumina1.3+/Illumina1.5+ format.
@HISEQ:157:C6U61ANXX:3:1101:1680:2160 2:N:0:GTCCGCACTCTTTTCC
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