Templates with revision indicates that the components or processes have undergone comprehensive parameterization and testing.

Templates with revision indicates that the components or processes are currently being tested. There is some test data available, but there are parameters that need to be set up manually within the code.

Templates with revision indicates that the components or processes are not fully tested. There is no test data available, parameters need to be set up manually within the code, and specific code changes are required based on the data used.

Guidelines for downstream analysis

• Set the working directory to the directory containing this README. We recommend using a Project in Rstudio.
• Use install_dependencies.R to install all packages used in these reports.

nf-core pipelines

These templates assume that the raw data has been processed by

• nf-core/chipseq

Quick Start

With Rstudio

source(install_depedencies.R)

Downstream analysis

Before using any template: 1. Modify information.R with the right information. You can use this file with any template to include the project/analysis information. 2. Modify params.R with the locations of select files/folders from the output of nf-core/chipseq. These nf-core outputs will become inputs to various templates. 3. Modify the YAML header of the Rmd files to choose the right parameters for that report.

Additional useful info: - params*example.R are files containing parameters pointing to a small, simple dataset that can be used to test the report code and see how the fully rendered report looks.

Quality assessment

chipseq/01qualityassessment/QC.Rmd is a template for QC metrics. It includes basic read-level statistics, peak quality information, sample correlation analysis, and PCA that it produces using the above samplesheet and output from the nf-core pipeline. Use params_qc.R to provide the required input files.

Differential expression

chipseq/02_diffbind/diffbind.Rmd

On the YAML header file of the Rmd you can specify some parameters or just set them up in the second chunk of code of the template.

On the YAML header file of the Rmd you can specify some parameters including the conditions to be compared, the genome used, and the desired output file names. This template has examples of: * calculating a peak counts matrix * PCA * differential binding analysis * peak annotation * functional analysis (coming soon)

This template writes to CSV a log2 normalized counts matrix of peaks x samples as well as the annotated significant results of the differential binding analysis.