Genome-wide quantification of differential transcription factor activity: diffTF

Thank you for the interest in diffTF! If you have questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation.

Summary

Transcription factor (TF) activity constitutes an important readout of cellular signalling pathways and thus for assessing regulatory differences across conditions. However, current technologies lack the ability to simultaneously assessing activity changes for multiple TFs and surprisingly little is known about whether a TF acts as repressor or activator. To this end, we introduce the widely applicable genome-wide method diffTF to assess differential TF binding activity and classifying TFs as activator or repressor by integrating any type of genome-wide chromatin with RNA-Seq data and in-silico predicted TF binding sites

Documentation

A detailed Documentation is available here

Installation and Quick Start

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``

4. To run your own analysis, modify the files config.json and sampleData.tsv. See the instructions in Section 3 in the Documentation for more details.
5. 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 into Section 4 in the Documentation to troubleshoot.

Citation

Please cite the following article if you use diffTF in your research:

Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Rassmussen & Judith B. Zaugg. Genome-wide quantification of differential transcription factor activity: diffTF. 2017. submitted.