I am new to using Qiime and am trying to work through the pipeline with some 16S V4 paired-end sequencing reads. I have got as far as demultiplexing the data.
Comparing the per-sample sequence counts between those produced by Qiime 2 demultiplexing and those produced by BaseSpace, I noticed that the BaseSpace per sequence counts are far higher with nearly all samples with totals a lot higher than 1000. Whereas, for Qiime2 the vast majority of samples have counts less than 1000.
Therefore, I was wondering what could be causing this discrepancy in the demultiplexing results. Am I doing something wrong in the Qiime 2 command line?
My sequences were produced using the EMP protocol and consists of paired-end reads with a single 12bp barcode on the forward primer
I am running Qiime2-2021.8, installed via Conda.
To import the files I used the following commands:
qiime tools import --type EMPPairedEndSequences
To demultiplex I used these commands:
qiime demux emp-paired
Thanks for any light you can shed on this issue