Project 3: Individual Project

For the final project, we will provide you a choice of datasets that we will ask you to analyze and explore. You will need to construct a working snakemake workflow that performs the appropriate processing steps and produce any required deliverables. We will give you all of the necessary details to perform the analysis, but we will not tell you the source of the data. You will perform a basic analysis and be asked to draw some high-level biological conclusions based on the results you generate.

There are three datasets representing a RNAseq, a ChIPseq and an ATACseq dataset. We haven’t worked with ATACseq data directly, so choose this option if you want an extra challenge. I will provide some hints for ATACseq specifically, but you will be asked to figure out how to perform some additional steps on your own.

Project Proposal

To help guide you, you will write a short project proposal outlining what you will be doing to process the data. We will give you feedback on your plan and then you will need to follow the instructions for each dataset in terms of what you will be asked to deliver. The proposal should be no longer than 1 page and include the following:

1. A detailed methods section that describes the exact steps you will perform in your workflow.
   • This should include specific software tools and their versions
   • Include any optional parameters that would affect the reproduction of your analysis
2. A list of the questions you will address and the deliverables you will produce for each project.
   • You may simply copy these from this proposal page.
   • This is just to make it clear exactly what you need to produce / address in the course of your analysis

Please make this proposal your README on the github repo you create for this project. You can look at the example below to get a sense for what it should include and there will also be a sample report so you have an idea of how to format your results.

https://github.com/BF528/bf528-individual-project-joeyorofino

Universal Project Requirements

Your submission will be a github repository with a single snakefile that represents your entire workflow. Please accept the github classroom link and your repo should contain at minimum the following at completion:

1. A single snakefile that performs all of the necessary steps of your workflow.

2. An envs/ directory with .yml files that specify the environments and packages each of your snakemake rules will utilize.

   • You may simply copy the .yml specifications for different packages from the previous projects.
   • If you need to use a different tool, you can simply create a new .yml file in the same style as the others

3. A jupyter notebook or Rmarkdown that summarizes the findings of the experiment:

   • This will include any discussions requested in the project description
   • This will include any figures / plots requested in the project description
   • This may also include any steps that are not easily incorporated into a snakemake workflow
   • The full methods section with any corrections from the initial proposal

The github classroom link is here: https://classroom.github.com/a/8-QdghaF

The data for each project can be found in our class directory at:

/projectnb/bf528/materials/project_3_individual/{atacseq/chipseq/rnaseq/}

Table of Contents

RNAseq

ChIPseq

ATACseq