Duke High Throughput Sequencing Course Materials

Duke University’s Department of Biostatistics and Bioinformatics hosted a summer course in High-Throughput Sequencing (HTS) during the summers of 2017-2019. The course was made possible through an NIH R25 training grant as part of the Big Data to Knowledge Initiative (BD2KI).
The course materials are made public here in three different formats:

1. A static webpage. Here, users can simply browse the course documents and copy-and-paste sample code.

2. A docker image together with Jupyter notebooks. The docker image contains all the necessary software to execute the notebooks. It may be used as learning materials, but also may be utilized as a self-contained execution environment for RNA-seq data analysis.

3. A Binder repository. Binder provides an execution environment (in the form of a docker container) for users to execute Jupyter notebooks ‘on the fly’. This is a great option for running through the R and Unix tutorials, and for some of the analysis pipeline. However, please note that this option can be a bit problematic. Some of the notebooks will fail due to missing fastq files. They are too large to load on Binder. To run the entire pipeline, option 2 is best.

Research reported in this website was supported by the National Institute Of Biomedical Imaging And Bioengineering of the National Institutes of Health under award number R25EB023928.

For questions or comments, please contact Janice McCarthy.