This repository contains all code used for the preparation and analysis of RNA sequencing data from an RNA sequencing time series experiment on Aplysia californica sensory neurons in the lab of Dr. Lynne Fieber at the University of Miami Rosenstiel School of Marine and Atmospheric Science. This repository consists mainly of the R project hierarchy and associated files and scripts used during this analysis, with inclusion of BASH scripts used for raw read processing, cleaning, and mapping-quantification steps on a HPC cluster.
The associated publication can be found here:
Kron NS, Schmale MC and Fieber LA (2020) Changes in Metabolism and Proteostasis Drive Aging Phenotype in Aplysia californica Sensory Neurons. Front. Aging Neurosci. 12:573764. doi: 10.3389/fnagi.2020.573764
Author: Nicholas Kron - n.kron@umiami.edu
Maintainer: Nicholas Kron - n.kron@umiami.edu
data -- : directory for data used in downstream R analysis
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--annotation_data : raw annotation files for building annotation objects in R for downstream analysis
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--metadata : metadata on animals, RNA extractions, and samples used in downstream R analysis
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--r_data : destination for storage of intermediate R data. (not presents as listed in the gitignore file)
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--salmon_files : destination for abundance estimates generated by the linux program salmon. (not presents as listed in the gitignore file)
figures -- : destination for figure output of R analysis
results -- : destination for results files of R analysis
scripts -- : scripts used for data analysis in this study
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-- bash : BASH scripts used for raw read processing, cleaning, and mapping-quantification steps before R analysis. Scripts are written to run on the University of Miami's HPC cluster PEGASUS and will need to be modified to run on other systems.