Hello everyone.
I am a university student who has started to do research on intestinal microbiome.
I am analyzing 16 fecal samples, and I have created a manifest file and then got a qzv file using the following command, but when I look at the resulting qzv file, forward and reverse appear respectively.
When I analyzed another sample with the same command before, forward and reverse were not separated.
Are forwad and reverse not merged?
I was hoping you could give me a solution.
Q2-demux doesn't join paired-end reads. You can do that during denoising with DADA2 (example), or you can do your own qc and join them with q2-vsearch.
You can use the 'Provenance' tab of your prior visualization to see what your commands were, and deduce why you don't have forward and reverse reads there.
As I mentioned above, when I used another samples in same command before, it was not necessary to join paired-end reads. Do you know why this is?
Sample files and manifest files look same, like
S1 /Users/inukaiyousuke/Desktop/qiime2/ngs1/1730_S22_L001_R1_001.fastq.gz forward
S1 /Users/inukaiyousuke/Desktop/qiime2/ngs1/1730_S22_L001_R2_001.fastq.gz reverse
.......
I used Provenance tab in both qzv files, action details looks same for me.
If you'd like to share the one with only one set of reads, I can take a look and let you know what I think. Here is great, or by private message if you're concerned about sharing too broadly.
I'm sorry.
Now that I checked, the problem seemed to be that the sample ended up at 150 sequence base.
The correct sample is up to 300 sequence base.
From here, I can proceed to denoise in the normal way, right?
Sorry for the late reply.
Here is my demux-summary.qzv.
These are 2x300 paired-end reads.
qzv shows forward read and reverse reads, but both same sequence counts.
Is this correct?
In next step, I'm going to try denoise using p-trunc-len-f 295 --p-trunc-len-r 250.
Thanks for sharing those visualizations, @yokmok. LEN.qzv was created with a rather old version of q2-demux (2019.7), while startate.qzv was created with something more recent.
If you click on the "Interactive Quality Plots" tab in either viz, you'll see that F/R reads are there in both - you'll have to join your reads downstream of demuxing in either case.
