Confused about demux.qzv for getting two quality plots i.e. for forward reads and reverse reads in the interactive quality plot tabs?

[Aqleem12 (Virtue)]

In the demultiplexed section, when I view demux.qzv I get two quality plots one for forward reads and other for reverse reads. Now I donot whether I am wrong or right. Further I donot know which parameters I used for sequence quality control?

[wasade (Daniel McDonald)]

Hi @Aqleem12, thank you for reaching out. There isn’t really a right or wrong, but some downstream methods may have different expectations. In the case of DADA2, as I understand it, quality filtering is not necessary. For Deblur, we advise at least minimal filtering with q2-quality-filter (e.g., the default parameters).

If you haven’t read it yet, you may be interested in Bokulich et al 2013 which explores the impact of PHRED filtering, and which forms the basis for the parameters used by q2-quality-filter.

Best,
Daniel

[jairideout (Jai Ram Rideout)]

Locking this duplicate topic and moving further support here:

I donot know how to truncate paired sequence bases. How do we know about the quality of the bases is high or low?

In the demux.qzv quality plots, i.e . two quality plots one for forward and one for reverse. I donot know how to truncated both quality plots. I have attached the file. Please help me in sequence quality control I used the command as follows;qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-trim-left 0 --p-trunc-len 120 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza [image]