In the FMT tutorial, denoising is done with DADA2 denoise-single.
We’ll begin by performing quality control on the demultiplexed sequences using DADA2, but this time we’ll run the
denoise-singlecommand on each set of demultiplexed sequences individually.
However, in the original paper it says:
A 16S rRNA library for MiSeq Illumina platform was prepared according to the protocol from Earth Microbiome Project. The barcoded primer set 515f-806r were used for pair-ended sequencing to target the 16S rRNA V4 region
EDIT: The raw, unpaired fastq files are in the starting node of processing network:
I looked up the study in Qiita, but can't find the paired-end data anywhere.
Does anyone have the paired end data for this project?
Does anyone know why only the forward reads are used in the official FMT tutorial?