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Differential ATAC-seq toolkit

Project description

# DAStk

The Differential [ATAC-seq](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/) Toolkit (DAStk) is a set of command-line tools to aid analyzing differential ATAC-seq data. By leveraging changes in accessible chromatin, we can detect significant changes in transcription factor (TF) activity. This is a simple but powerful tool for cellular perturbation analysis. In fact, the applications of DAStk are not necessarily limited to ATAC-seq, but can extend to comparing any pair of bedGraphs containing regions of interest, like transcription regulatory elements (TRE) from nascent transcription assays like PRO-seq, or others like ChIP-seq peaks.

You will need the following inputs:

  • A pair of files listing peaks of ATAC-seq signal in two biological conditions (e.g. DMSO and drug-treated) in any BedGraph-compatible format (tab-delimited)
  • A set of files listing the putative binding sites across the reference genome of choice, one file per transcription factor motif, also in any BedGraph-like format. These are normally generated from position weight matrices (PWMs) available at TF model databases like [HOCOMOCO](http://hocomoco11.autosome.ru). These files are expected to have a .bed, .BedGraph or .txt extension.

IMPORTANT: All files mentioned above (ATAC-seq peaks and computed motif sites) MUST be sorted by the same criteria. Different bioinformatics tools use different lexical sorting criteria (e.g. chr10 after chr1, or chr2 after chr1) so please ensure the sorting criteria is uniform.

### Install

You can install DAStk using pip:

$ pip install DAStk

This is the simplest option, and it will also create the executable commands process_atac and differential_md_score. Alternatively, you can clone this repository by running:

$ git clone https://biof-git.colorado.edu/dowelllab/DAStk

### Required Python libraries (automatically taken care of if installed thru pip):

  • numpy
  • argparse
  • matplotlib
  • scipy
  • adjustText
  • pandas
  • multiprocessing
  • pybedtools

These scripts feature comprehensive help when called with the –help argument. Every argument provides a short and long form (i.e. -t or –threads). There are normally two steps in a typical workflow:

  1. Process the ATAC-seq peak files to calculate the [MD-score statistic](https://genome.cshlp.org/content/28/3/334.short) for each motif provided.
  2. Detect the most statistically significant changes in MD-score between both biological conditions (taking into the account the peaks involved), and generate MA and barcode plots.

### TL;DR;

Process each ATAC-seq peak bedGraph file, the genome abbreviations are “hg38”, “mm10”, etc:

$ process_atac -e PEAKS_FILENAME_1 -m MOTIF_SITES_DIRECTORY -g GENOME_ABBREVIATION -o OUTPUT_DIRECTORY $ process_atac -e PEAKS_FILENAME_2 -m MOTIF_SITES_DIRECTORY -g GENOME_ABBREVIATION -o OUTPUT_DIRECTORY

Perform differential analysis on the calculated motif displacement scores, highlighting the significant motifs at your p-value threshold of choice:

$ differential_md_score -1 MD_OUTPUT_FOR_FILENAME_1 -2 MD_OUTPUT_FOR_FILENAME_2 -p 0.0000001 -m “DMSO” -n “Drug treatment” -b -o OUTPUT_DIRECTORY

Questions?

$ process_atac –help $ differential_md_score –help

### Usage examples

Unpack the motif files (see below for how to create your own, instead):

$ mkdir /path/to/grch38_motifs $ tar xvfz motifs/HOCOMOCO_v11_p1e-6_grch38.tar.gz –directory /path/to/grch38_motifs

Calculate the MD-scores for the first biological condition:

$ process_atac –threads 8 –atac-peaks /path/to/DMSO/ATAC/peaks/file
–motif-path /path/to/directory/containing/motif/files –output /path/to/output/directory

The above command generates a file called BASENAME_md_scores.txt. It’s generally a good idea to use the cell type (or sample number) and a brief condition description (e.g. k562_DMSO or SRR1234123_Metronidazole) in the file name provided.

We would then generate the same file, for the other biological condition we are comparing against:

$ process_atac –threads 8 –atac-peaks /path/to/treatment/ATAC/peaks/file
–motif-path /path/to/directory/containing/motif/files –output /path/to/output/directory

The above generates a file called BASENAME_md_scores.txt. Finally:

$ differential_md_score –assay-1 DMSO –assay-2 Treatment –p-value 0.0000001 –barcodes –output /path/to/output/directory

The above generates a tab-delimited file with all differential MD scores for each motif and their p-values (sorted by p-value), an MA plot that labels the most significant TF activity changes, at a p-value cutoff of 1e-7. Note that better plot-friendly condition names (say, DMSO and Treatment) can be provided using the –label-1 and –label-2 arguments. The plots look like the example below:

![Sample MA plot](./doc_files/sample_MA_plot.png)

The -b flag also generates a “barcode plot” of each of these statistically significat motif differences that depicts how close the ATAC-seq peaks were to the (putative TF-binding) motif sites, within a 1500 base-pair radius of the motif center:

![Sample barcode plot](./doc_files/sample_barcode_plot.png)

If you can take advantage of multiprocessing, you can calculate MD-scores for both conditions simultaneously, assigning several threads to each, then generate the plots once both *_md_scores.txt files are ready.

### Motif Files

Feel free to use the pre-scanned motif files provided, [HOCOMOCO_v11_p1e-6_grch38.tar.gz](http://dowell.colorado.edu/pubs/DAStk/HOCOMOCO_v11_p1e-6_grch38.tar.gz), [HOCOMOCO_v11_p1e-6_hg19.tar.gz](http://dowell.colorado.edu/pubs/DAStk/HOCOMOCO_v11_p1e-6_hg19.tar.gz) and [HOCOMOCO_v11_p1e-6_mm10.tar.gz](http://dowell.colorado.edu/pubs/DAStk/HOCOMOCO_v11_p1e-6_mm10.tar.gz) for the GRcH38, hg19 and mm10 reference genomes, respectively. They have been generated from HOCOMOCO’s v11 mononucleotide model, background-corrected for each reference genome. To generate your own bed files for each motif from this or any other source, you can use FIMO in combination with the downloaded .meme files from your TF database of choice. For example, if using HOCOMOCO, you can create the motif file for TP53 using their mononucleotide model with a p-value threshold of 0.000001 by:

$ fimo -max-stored-scores 10000000 –thresh 1e-6 -oc /path/to/output/directory -motif /path/to/motif/file
/path/to/HOCOMOCOv11_HUMAN_mono_meme_format.meme /path/to/whole_genome.fa

Please refer to the complete [FIMO](http://meme-suite.org/doc/fimo.html?man_type=web) documentation for any questions.


### Citation

Please cite DAStk if you have used it in your research!

Tripodi, I.J.; Allen, M.A.; Dowell, R.D. Detecting Differential Transcription Factor Activity from ATAC-Seq Data. Molecules 2018, 23, 1136.

If you have used the provided scanned motif regions from HOCOMOCO, please cite them as well:

Kulakovskiy, I.V., Vorontsov, I.E., Yevshin, I.S., Sharipov, R.N., Fedorova, A.D., Rumynskiy, E.I., Medvedeva, Y.A., Magana-Mora, A., Bajic, V.B., Papatsenko, D.A., et al. (2018). HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Res 46, D252–D259.

For any questions or bug reports, please use the Issue Tracker or email us:

Ignacio Tripodi (ignacio.tripodi at colorado.edu) Computer Science Department, BioFrontiers Institute University of Colorado, Boulder, USA

Margaret Gruca (margaret.gruca at colorado.edu) BioFrontiers Institute University of Colorado, Boulder, USA

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