Quality plot after importing data

[gsshankar (Shankar Shanmugam)]

Hello Experts,

Please see the attached qzv file that I got after running the qiime demux summarize command. The quality plot doesn't run smooth and has discrete bars. Please check if there is some wrong with the sequences that I got from the sequencing facility.

The command that i ran

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path ccmtbac
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path ccmt-demux-paired-end.qza

qiime demux summarize
--i-data ccmt-demux-paired-end.qza
--o-visualization ccmt-demux-paired-end.qzv

ccmt-demux-paired-end.qzv (313.5 KB)

Thanks,
Shankar

[SoilRotifer (Mike Robeson)]

Hi @gsshankar, welcome to :qiime2:!

It appears that these may have been pre-processed in some way. Are you sure these are the raw data files? This appears quite similar to what is discussed in this thread:

DADA2 for Single-end sequences from .FASTQ

Yep, as I suspected — it is indeed that the Q-scores are all uniform (presumably in all sequences, not just the first few). This is impossible — it indicates that the authors of the study most likely created artificial Q scores for the reads, possibly because the original quality scores were lost. You could contact them for the true Q scores/explanation. So these data will not work with dada2. You could use deblur (which does not use Q scores) for denoising. Good luck!

-Mike