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Weird Basecalled reads PHRED quality plot from pycoQC

I'm using pycoQC to get some metrics on a nanopore sequencing run. I did the basecalling with dorado with bam as output, dorado summary to get the sequencing_summary.txt file that I pass to pycoQC to generate the report. In the report I get this basecalled reads PHRED quality plot: enter image description here

I though it looked a bit funky so I checked how it usually looks like and it doesn't have this spikes, it's normally a kind of smooth distribution. I've run also NanoPlot and from the plots generated I can see that all the read qualities are whole numbers.

I also got this plot for the read length which looks too uniform. enter image description here

I don't know if this is normal (I don't think so), if this is a common thing because I did something wrong or this is just weird. Any help would be appreciated.

pycoqc nanopore sequencing
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written by njornet • njornet

Interesting. Do you have access to the original sequencing summary file from the sequencer (even if FAST basecalling was used)? What does that look like compared to this?

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written by GenoMax GenoMax

They didn't perform basecalling with the sequencer if that's what you are asking. I've found a file within the sequencer output folder called "sequencing_summary_FAR92635_867dc3b7.txt" but when I run pycoQC with it I get this error

pycoQC.common.pycoQCError: Column read_len not found in the provided sequence_summary file

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written by njornet • njornet

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