Long read data trimming

Hi!

I'm trying to analyze taxonomy assignment using long read sequencing data generated from Illumin HiSeq, PacBio, and Nanopore.
My workflow gonna be like this, roughly:
Import - dada2(single) - taxonomy assign.
This is my first time using long read sequencing data, what I'm wondering is,
which is appropriate position for dada2 to truncate the data?
When I use amplicon sequences, I made position where 25%-tile goes under Q20 first, but it does not seems to apply at long read.

Any suggestions will be appreciate.

Thank you!
EY

This full analysis article shows these settings for PacBio

filterAndTrim(nops2, filts2, minQ=3, minLen=1000, maxLen=1600, maxN=0, rm.phix=FALSE, maxEE=2)

Perhaps you already found these during your lit review.

For my own notes, here is the DADA2 PacBio paper:

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.