Weird result in Demultiplexed sequence counts summary


I have recently started to work on microbiome data and this is my first post.
Hope this is not a duplicated subject.

My data consists of two FASTQ files:
159-78_S76_L001_R1_001.fastq & 159-78_S76_L001_R2_001.fastq.
After trying the different import methods, the following seems work for those:
qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path manifest \
–output-path demux_91.qza \
–input-format PairedEndFastqManifestPhred33

with the corresponding manifest file:

The thing is that if I create a summary for the sequence,
then it contains only one samples, called “sample-1”,
so that no histogram at all and this 112866 is the only number on the summary stats.

I am not sure whether I was using the right procedure for the import.
Would you please give me some inputs on this?
Any advice would be very appriciated.

Thank you!

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I think my manifest file has a problem; so,
I changed it as follows:

But, after this, I still got a similar result only one number appears.

Hi @fblues,

So your 2 fastq files are from the same sample, one is your forward and one is the reverse reads. When you import these using the manifest format you are telling qiime just as much, that these 2 samples are paired. Therefore the summary visualization just shows 1 sample, which is correct. I’ve never personally tried creating a visualization with only 1 sample, I would still expect to get a quality plot as those those plots are made by randomly sampling 10,000 sequences from the total pool. Maybe this is a bug that precludes the creation of quality plots for 1 sample. Let’s see what the devs say on the matter. In the meantime though it would be helpful if you could share with us the summary visualization artifact. Otherwise I don’t think you’ve done anything wrong.

Thanks @Mehrbod_Estaki!

No, this is deliberate --- there is nothing to show when there is only one sample:


That square is expressed via the other summary metrics, so no need for the plugin to plot it. @fblues, the more important part of this step is arguably the interactive quality plot tab in that viz --- does everything look okay there? :t_rex:

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