Originally posted by jkbonfield
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I just wrote a quick Perl script to check how N is being qualitied on a recent Pipeline 1.6 for the first 2M reads of a random fastq file from the run (QVALUE => FREQUENCY):
'6' => 7,
'11' => 22,
'7' => 57,
'9' => 80,
'12' => 18,
'2' => 281517,
'15' => 1,
'14' => 5,
'8' => 62,
'4' => 51799,
'13' => 3,
'10' => 23,
'5' => 72
As you can see, most are Q02, which is "B" and is part of the 'rejected section' of the read, so they can be ignored. Most of true Ns are Q4 ("D") as they were in your experience, however there are still smatterings of Ns with qualities all the way up to Q15 !
*sigh*
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