This repo provides pipeline, R code and other materials, used in the manuscript titled:

Inter- and intra-annual bacterioplankton community patterns in a deepwater sub-Arctic region: persistent high background abundance of putative oil degraders

Angelina G. Angelova1, Barbara Berx2, Eileen Bresnan2, Samantha B. Joye3, Andrew Free4, Tony Gutierrez1

1School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK

2Marine Scotland Science, Aberdeen, AB11 9DB, UK

3Department of Marine Sciences, University of Georgia, Athens, Georgia, USA

4School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK

A 16S-based analysis (V3-V4 rRNA gene region) of microbial communities found in the water column of the Faroe-Shetland Channel (FSC)

Information about files provided:

All files starting with DB are the SINTAX-formated database files used for assigning taxonomy.
DB_ncbi16S.fasta was used for the FSC baseline taxonomic assignment. The rest of the provided are supplemental.

pipeline.txt file provides the general structure of the bioinformatics pipeline

zASV_OTUtab-nonchim.txt = the ASV counts table produced by VSEARCH after chimera removal
zASV_TAXtab-nonchim.txt = the TAXONOMY asignments for each ASV (Its been cleaned with: cut -f1,3 -d "\t" | sed 's/;*\t/\t/g' )
zASV_SEQfa-nonchim.txt = the fasta file of the nonchimeric ASV sequences

SampleMapping.xlsx file contains the "everything" metadata file

metadataR.txt is a shorter version of the metadata file, formated for R

zASV_Ranalysis_v314.7.Rmd is the R script used to genarate the analysis + some explanations .. and ranting

DESeq / differential abundance analysis results tables
DeSeq-WO-Season.csv - Seasonal variaion of taxa within the different Water Origins \