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3 hours ago by

Dear all,

I got some Illumina data in from an external provider. It seems it's from a NovaSeq (instrument ID starts with @A00, and according to that post...)

So, it's paired-end RNA sequencing data (2x151bp), prepared with the TruSeq Stranded mRNA LT Sample Prep Kit following the protocol "TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E". I'm surprised to see the quality scores look like that:

or like that:

or like that:

Of course 'F' is a very good score (Q37), but ':' is only Q25, and ',' is even worse (Q11). Have you guys observed such very short basecalling quality dips in otherwise good-looking RNA-based data?

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