Genomic Data

Course Overview

Course Integrity

This course is compiled automatically on 2021-03-07

The course is tested and available on MacOS, Windows and Ubuntu Linux for R version 4.0.3 (2020-10-10)

Overview

This course introduces typical genomic file formats from high-throughput sequencing data.

The course consists of 2 sections and should be pre-requisite to ChIP-seq or RNA-seq courses. The 1st section outlines the common data formats used in the analysis of genomics data. The 2nd section is an overview of public repositories that store published data.

Course material and exercises are available to view as rendered HTML at http://rockefelleruniversity.github.io/Genomic_Data/. All material is available to download under GPL v3 license.

Setting up

System Requirements

Install R

R can be installed from the R-project website.

The R website can be found here http://www.r-project.org/.

The download links and associated installation instructions for multiple platforms can be found below provided by Revolution Analytics. https://cran.revolutionanalytics.com

We recommend installing R 4.0.3 as this is the version used to compile the course. Direct downloads for R 4.0.3 for the main platforms can be found below:

Install required packages

From the course package

install.packages('BiocManager')
BiocManager::install('RockefellerUniversity/Genomic_Data',subdir='GenomicsData')

From CRAN and Bioconductor

install.packages('BiocManager')
BiocManager::install('methods')
BiocManager::install('rmarkdown')
BiocManager::install('knitr')
BiocManager::install('testthat')
BiocManager::install('yaml')

Download the material

The Presentations

Genomic Data Formats

This section focuses on the file formats commonly used in genomics analysis and what they used for:

Reference Genomes
Sequences
Summary Data

Links to presentations:

The html slide presentation can be found at this link Slide

The single page html presentation can be found at this link Single Page

The code use in the presentations can be found at R code

Genomic Data Repositories

This section focuses on where you can get different types of published genomic data.

Links to presentations:

The html slide presentation can be found at this link Slide

The single page html presentation can be found at this link Single Page

The code use in the presentations can be found at R code

Getting help

Course help

For advice, help and comments for the material covered in this course please contact us at the issues page associated to this course.

The link to the help pages can be found here

General Bioinformatics support

If you would like contact us about general bioinformatics advice, support or collaboration, please contact us the Bioinformatics Resource Center at brc@rockefeller.edu.