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
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
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 -
presentations generated using R
- Part 1: Behavioral analysis
- Part 2: RNA sequencing analysis
Download the data to scratch on Stampede with
- 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
- UNIXworkflow/00_rawdata: Download the data to scratch on Stampede with
- 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.