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2brad_utilities

A collection of scripts for analyzing 2bRAD genotyping data.

annotatingtranscriptomes

Assembly and annotation of transcriptomes de novo

convergent_evo_coral

assign orthologs and test for molecular convergence in coral transcriptomes

deseq_custom

Example R script and input files for running a standard differential expression analysis using DESeq and generating summary plots

filteringtranscriptomes

Scripts and walkthrough necessary to assemble and filter a holobiont transcriptome

go_mwu

Rank-based Gene Ontology analysis of gene expression data

irma

This project tests whether hurricane-driven fragmentation and survival patterns correlate with the existing clonal structure across coral species, to evaluate the long-term impact of storms in contributing to asexual propagation of Florida corals.

montisymtransgen

poriteswps

global gene expression patterns in WPS affected tissues

pseudo-nitzschia2brad

Pseudo-nitzschia spp. produces a neurotoxin, domoic acid (DA), which can cause illness in humans, commonly known as amnesic shellfish poisoning, mass-mortality of marine animals, and closure of commercial shellfish fisheries during bloom events. Understanding and forecasting these harmful algal blooms is a primary management goal; however, accurately predicting the onset and severity of Pseudo-nitzschia bloom events remains difficult, in part because the underlying drivers of bloom formation have not been fully resolved. Recent work suggests that the genetic composition of a Pseudo-nitzschia bloom may be a better predictor of toxicity than prevailing environmental conditions. Here, we test the ability of reduced representation sequencing (2b-RAD) to delineate inter and intra-species level genetic variation of Pseudo-nitzschia. We generated 2bRAD libraries from pure cultures of Pseudo-nitzschia spp. and mock community mixes. We also generated sequencing libraries from longitudinal field samples from the San Pedro Shelf. This repository contains the bioinformatic and statistical scripts necessary to re-create analyses, as well as raw input data used to generate figures. FASTQ reads for both the Mock Community Mix (SUB9673624) and Natural Sample libraries (SUB10064804) can be obtained from NCBI’s SRA under BioProject PRJNA749297. The final Pseudo-nitzschia spp. 2bRAD reference library is hosted at https://dornsife.usc.edu/labs/carlslab/data/.

spatial-heat-maps-in-r

Create spatial heatmaps to illustrate the relative percent change in coral cover over time at a given location.

tag-based_rnaseq

Cost-efficient genome-wide gene expression profiling

usc_hpc_scripts

a USC-specific set of scripts needed for Tag-Seq and 2bRAD processing