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
qiime demux summarize
ccmt-demux-paired-end.qzv (313.5 KB)
@gsshankar, welcome to !
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:
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.
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