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Old 04-24-2010, 08:21 PM   #3
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Location: The University of Melbourne, AUSTRALIA

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Originally Posted by Bio.X2Y View Post
I'm having a look at some FASTQ files generated from the Illumina GA pipeline (I think version 1.3).
(2) is it normal to have a non-zero lower bound for observed quality scores (in our case, 2)?
(3) is there an obvious reason why none of our bases has a quality of 3, even though every other quality in the range 2 to 34 is highly represented?
Perhaps it is related to this new 'feature' of Pipeline 1.3+? See SLIDE 17 in Here is the text of the slide:

"The Read Segment Quality Control Indicator: At the ends of some reads, quality scores are unreliable. Illumina has an algorithm for identifying these unreliable runs of quality scores, and we use a special indicator to flag these portions of reads A quality score of 2, encoded as a "B", is used as a special indicator. A quality score of 2 does not imply a specific error rate, but rather implies that the marked region of the read should not be used for downstream analysis. Some reads will end with a run of B (or Q2) basecalls, but there will never be an isolated Q2 basecall."
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