OKyne1
commented
9 months ago Yep I encountered this problem too and spent a long time trying to find missing reads. Thanks for pointing it out valery-shap.
It looks like you can specify the min pass value in pycoQC. So as long as you use this then it shouldn't be an issue
Hello,
version of PycoQC 2.5.2. There are no errors, but the number of reads by barcode in html file is different from counting by other methods. I tried to count pass reads by bash (zcat |wc -l) /4|bc and I parsed the sequencing_summary file with conditions: 'barcode_arrangement' == 'barcode02' & 'passes_filtering' == True The number is identical between counting by bash and parsing. What could be the mistake? Upd I counted the reads that PASS the guppy filter: "The minimum q-score a read must attain to pass qscore filtering. The default value for this varies by configuration: for faster models it is 7.0, roughly corresponding to an accuracy of 85%, and is higher for more accurate models. This should have a minimal impact on output." I had the accurate basecalling model. So the limit for filtering is not always 7.0 and I suppose that PycoQC counts the reads that have mean_qscore_template > 7
Best regards, Valery