(16s) No 0. Raw 16S rRNA fastq data files for Bocas hypoxia study

This repository contains the **RAW** sequencing data for hypoxia study.
Trimmed reads (with primers removed) are deposited at the European Nucleotide
Archive, study accession number **PRJEB36632 (ERP119845)**.

Raw fastq data files are named using the root format RunQ_XYZ, where Q is the
run number (1, or 2), **X** is the habitat type (**C** oral, **W** ater, **S**
ediment, **M** at), **YZ** is the site (CC = Coral Cay; CR = Cayo Roldan), and
in some cases a replicate number.

So...

Run01_CCR1_R2_001.fastq

...corresponds to the reverse reads (R2) of a Cayo Roldan (CR) coral sample
(C), replicate #1, Run 1.

**Raw fastq files are deposited here by Run.**

We used the PowerSoil® DNA Isolation Kit (MoBio) following the manufacturer's
protocol to extract community DNA from each sample.

Extracted DNA was sequenced on an Illumina MiSeq by Integrated Microbiome
Resource at the Centre for Comparative Genomics and Evolutionary
Bioinformatics (Dalhousie University).

We targeted the V4-V5 hypervariable region using 515F (5′-GTGYCAGCMGCCGCGGTA)
and 926R (5′-CCGYCAATTYMTTTRAGT). We collected 38 samples encompassing two
sites and four habitat types

We generated sequence data for all 38 samples. In the first run (Run01), all
samples were sequenced and, due to lower than average yield, several were re-
sequenced (Run02).

This repo also contains the metadata files for submitting the **trimmed** data
to the European Nucleotide Archive (ENA). Please do confuse this datasets with
the dataset archived on the ENA (accession number PRJEB36632). In order to
submit to the ENA, we had to first remove primers from the raw data and then
upload the data along with these metadata files.

The first publication concerns the water samples only. If you are interested
in those samples only they are also available in the WATER_ONLY.zip file.