Click the button to launch a Binder R session. Navigate to the scripts directory and open any .Rmd file.

Overview

This repo contains the experiment that I like to call “IntegrativeProjectWT2015” because it is an integrative analysis of behavior, electrophysiology, and RNA-seq data collected from wild type mice in 2015.

This research is undergoing peer-review at Hippocampus. A preprint is available at https://www.biorxiv.org/content/10.1101/2020.02.05.935759v1.

Please cite this GitHub repository as Rayna M Harris. (2017, November 29). raynamharris/IntegrativeProjectWT2015: GitHub Repository for the Integrative WT 2015 Project (Version v1.3). Zenodo. http://doi.org/10.5281/zenodo.1068356

Bioinformatics Workflow

This project is organized into five main subdirectories: - scripts: contains all the knitr-based R workflows for statistical analyses and data visualization (source code is in the .Rmd files, and .md files are used to visualize the code and the results - UNIXworkflow: contains and explanation and all the UNIX commands used to process the raw sequencing data on the Stampede cluster at the Texas Advanced Computing Facility - figures: all the figures created from the scripts - data: all the input data and the results - docs: presentations generated using R

• Part 1: Behavioral analysis
  • scripts/00_behavior_wrangle: behavior data wrangling
  • scripts/01_behavior_analysis: behavior statistics and data visualization
• Part 2: RNA sequencing analysis
  • UNIX-based
    • UNIXworkflow/00_rawdata: Download the data to scratch on Stampede with 00_gsaf_download.sh.
    • UNIXworkflow/01_fastqc: Evaluate the quality of the reads using the program FastQC.
    • UNIXworkflow/02_filtrimreads: Filter low quality reads and trim adapters using the program cutadapt.
    • UNIXworkflow/03_fastqc: Evaluate the quality of the processed reads
    • UNIXworkflow04_kallisto: Quantify transcript-level expression using Kallisto
  • R-based
    • scripts/00_rnaseq_wrangle: converting the kallisto transcript counts to gene counts
    • scripts/02_rnaseqQC: analyzing all the RNA-seq data together
    • scripts/03_rnaseqSubfield: analyzing the data for each hippocampal subfield separately
    • scripts/04_correlations.Rmd: correlations between genes and beahvior
    • scripts/05_GO an analysis of gene ontology.
    • scripts/06_candidates an analysis of candidate memory genes.