Try it out now!

The following quick start briefly summarizes the necessary steps to use our pipeline:

  1. Install the necessary tools (Snakemake, samtools, bedtools, and Subread). We recommend installing them via conda, in which case the installation is as easy as

    conda install -c bioconda snakemake bedtools samtools subread

    If conda is not yet installed, follow the installation instructions. If you want to install the tools manually and outside of the conda framework, see the following instructions for each of the tools: snakemake, samtools, bedtools, Subread.

  2. Clone the Git repository:

    git clone https://git.embl.de/grp-zaugg/diffTF

  3. To run the example analysis for 50 TF, simply perform the following steps:

  • Change into the example/input directory within the Git repository

    cd diffTF/example/input

  • Download the data via the download script

    sh downloadAllData.sh

  • To test if the setup is correct, start a dryrun via the first helper script

    sh startAnalysisDryRun.sh

  • Once the dryrun is successful, start the analysis via the second helper script

    sh startAnalysis.sh

  1. To run your own analysis, modify the files config.json and sampleData.ts. See the instructions in the section Run your own analysis for more details.
  2. If your analysis finished successfully, take a look into the FINAL_OUTPUT folder within your specified output directory, which contains the summary tables and visualization of your analysis. If you received an error, take a look in Section Handling errors to troubleshoot.

Prerequisites

This section lists the required software and how to install them. As outlined in Section Try it out now!, the easiest way is to install all of them via conda. However, it is of course also possible to install the tools separately.

Snakemake

Please ensure that you have at least version 4.3 installed. Principally, there are multiple ways to install Snakemake. We recommend installing it, along with all the other required software, via conda.

samtools, bedtools, Subread

In addition, samtools, bedtools and Subread are needed to run diffTF. We recommend installing them, along with all the other required software, via conda.

R and R packages

A working R installation is needed and a number of packages from either CRAN or Bioconductor have to be installed. Type the following in R to install them:

install.packages(c("checkmate", "futile.logger", "tidyverse", "reshape2", "gridExtra", "scales", "jsonlite", "RcolorBrewer", "rlist", "ggrepel", "lsr", "modeest", "locfdr", "boot"))
source("https://bioconductor.org/biocLite.R")
biocLite(c("limma", "vsn", "csaw", "DESeq2", "DiffBind", "geneplotter", "Rsamtools"))

Run your own analysis