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GenomiqueENS / toulligQC

A post sequencing QC tool for Oxford Nanopore sequencers
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Discrepancies between ToulligQC and PycoQC #29

Closed sklages closed 3 months ago

sklages commented 3 months ago

There are quite significant discrepancies between pycoQC and ToulligQC numbers and plots (based on passed data) when run on the same dataset.

That is probably due to the definition of "passed" for a read, that will most likely influence (all) subsequent calculations based on "passed" reads.

Can you provide a definition of what it needs for a read to be considered "passed" by ToulligQC?

alihamraoui commented 3 months ago

Hi @sklages,

A read is considered "passed" if its mean quality score is above a Phred score threshold. By default, this value is set to a Phred score of 9 in ToulligQC 2.7.

I believe the threshold in pycoQC is set to 7, which is why there are discrepancies between the ToulligQC and pycoQC numbers. You can adjust this value in ToulligQC using the --qscore-threshold flag.

We set it to 9 due to the significant improvements in the latest Nanopore chemistry.

Ali

sklages commented 3 months ago

@alihamraoui - thank you for clarification! That makes perfectly sense :-)