Question about manifest importing data

[spencer886 (Runzhi Zhang)]

Hi all,

I am new to QIIME2 and I am new to microbial data preprocessing.

I have my data like many paired-end samples, and I want to use three of them to test the data importing, the data looks like this (paired-end):

And I write a text file following the section “Fastq manifest” formats in Importing data tutorial :

I have successfully imported the data using the command:

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path camda_input.tsv
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2

And then I try to view the data using the command:

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

The results look like this:

I am just curious if the results are reasonable because the reads are too large for me compared to the results I saw from the tutorial.

Could someone help with this? Thanks!

[jwdebelius (Justine Debelius)]

Hi @spencer886,

The tutorial data has been curated to optimize run time, so the original reads were subsampled.

I'm personally a proponent of more shallow samples (5-10K post denosing) verse very few deep samples but ultimately that depends on your hypothesis.

Best,
Justine