Is there a way in Qiime2 to output QC plots for individual FASTQs as in dada2?
Using dada2 in R you'd import the samples, then plot quality scores for each individual file with plotQualityProfile(). The QZV output of qiime metadata tabulate on the dada2 denoising stats is a quality plot with the median scores of all samples. Viewing the individual FASTQs separately can help determine if there are individual bad samples that are obscured by median statistics.
If this doesn't exist already, I think it'd be helpful.
The only way I know how to output QC plots for individual .fq files is using qiime demux summarize command, however this is before the DADA2 step.
You can, however export your rep-seqs.qza and table.qza files, then import into R but that would be very similar (if not the same) as the method you have mentioned.
Once you have your rep-seqs.qza from DADA2, you could export them into a fasta format, convert into fastq, and then run them through FastQC.
I think it would also be helpful if it was built into Qiime. Cheers!
Hi @Mike_Stevenson. Yes, it seems that qiime demux summarize is pretty similar to the plotQualityProfile() from dada2. Maybe that's sufficient, but it would still be great to have it built in elsewhere too.
Yeah, there is not a great way to do this within Qiime2 right now.
This should work out:
There may be a bit of a disconnect here, as I don't think this would do it:
After running dada2, the ASVs no longer have quality scores. So while you can convert into fastq files, it's too late to make per-sample q-score plots.