# The wet lab protocol follows the DAMe protocol of Zepeda Mendoza, M. L., K. Bohmann, A. Carmona Baez, and M. T. P. Gilbert. 2016. DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses. BMC Research Notes 9:255.  

# This means that we subject each sample to three independent PCRs, with independent tags for each sample and each PCR.  
# We then use DAMe to filter out reads that appear in only one PCR. 

# Clone and unzip this repo in the root directory (or down a path where the folders have no spaces in their names)
# You will have a folder called 300TestTeaching/

# To download the fastq files:

> cd 300TestTeaching/data/seqs
> ls # you should see "list.txt"
> wget https://www.dropbox.com/s/31twk1qryjajhdo/Experiment_B.tar.gz?dl=1

# untar the downloaded file

> tar -xzvf 'Experiment_B.tar.gz?dl=1'
> rm 'Experiment_B.tar.gz?dl=1'

# You will have the following 6 fastq.gz files in the 300TestTeaching/data/seqs folder.
# B1_S4_L001_R1_001_0.1.fastq.gz
# B1_S4_L001_R2_001_0.1.fastq.gz
# B2_S5_L001_R1_001_0.1.fastq.gz
# B2_S5_L001_R2_001_0.1.fastq.gz
# B3_S6_L001_R1_001_0.1.fastq.gz
# B3_S6_L001_R2_001_0.1.fastq.gz