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wdecoster / nanocomp

Comparison of multiple long read datasets
MIT License
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reads above quality cutoffs #28

Closed LeilyR closed 4 years ago

LeilyR commented 4 years ago

Hi, May I ask, how I should interpret the numbers under the "Number, percentage and megabases of reads above quality cutoffs" section. Thanks a lot!

wdecoster commented 4 years ago

Reads are filtered for certain quality cutoffs, and the table lists the number of reads above that cut-off, the percentage of reads that are above that cut-off and the total contribution in megabases of those reads. Does that help?

LeilyR commented 4 years ago

thanks, so does it mean that if they are falling in >Q5 their quality is higher that 5? and this is the usual phred score right?

wdecoster commented 4 years ago

Yes, the category >Q5 is for reads with an average basecall Phred quality score above 5, obtained by converting all Phred scores of a read (of each base) to probabilities, taking the average of these probabilities and converting that back to the Phred scale.

LeilyR commented 4 years ago

Thank you so much for the clarification!