PairedEndSequence_Low quality_poor merge

Hi. I am using dada2 to denoise paired end sequence. The forward and reverse sequences are 300 nucleotides each. The merged data has only 0.02% of initial sequences when I truncate the sequence when it reaches quality less than 20 (around 190 bases). My question is, if I do not truncate to allow better merging, I am including reads that have values as low as 9. Can you suggest the best way to move forward in this case.

Welcome to the forum, @annalex!

You haven't given us much information about your data or the specific command you're running, but I suspect you may be overlooking DADA2's quality filtering step.

This topic goes into that briefly, and wisely suggests you consult your denoising-stats.qzv to diagnose sequence loss issues. The paper gets farther into the details. There are also tons of discussions of how to select DADA2 parameters here on the forum. Try reading up on the process a little, and let me know if you have questions.

Good luck!

Thank you Chris. The topics you suggested and some more deals with this issue. Thank you for the help

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