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Old 07-01-2013, 08:58 AM   #1
bob-loblaw
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Default What proportion of 'bad' quality reads are expected using HiSeq 2000 for RNA-Seq

I am just after processing 24 files, using trimmomatic to quality filter them. On average was 30% of the reads were bad quality (SD = 11).

This seems somewhat high to me, I was just wondering if anyone else had experience with this and could tell me what would be expected? If I should be particularly concerned about this...

Thanks.
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Old 07-02-2013, 10:31 AM   #2
westerman
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30% is indeed high. We -- I work at a sequencing center -- have seen such results but in these cases the problem is tracked down to sequencer problems, sample prep, or just an random problem. We almost always re-run the samples. Does fastQC show any particular place where the problem occurs?
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Old 07-02-2013, 10:45 AM   #3
GenoMax
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Hopefully these samples did not come from an overloaded flowcell. (Assuming that you have taken into account the right Q-score parameters for trimmomatic)
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