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atactk

A toolkit for working with ATAC-seq data.

What's in the box?

Programs we've found useful in analyzing ATAC-seq data

  • make_cut_matrix: useful in conjunction with CENTIPEDE, and in generating plots of transcription factor binding sites.
  • make_midpoint_matrix: useful in conjunction with CENTIPEDE, and in generating plots of transcription factor binding sites.
  • measure_signal: measures size and position of ATAC-seq fragments overlapping genomic features.
  • measure_features: given a bigWig file of coverage counts and a BED file of features, calculates a requested statistic for each feature.
  • plot_aggregate_cut_matrix.R: generates plots for motifs given the aggregate output of make_cut_matrix
  • plot_aggregate_midpoint_matrix.R: generates plots for motifs given the aggregate output of make_midpoint_matrix
  • plot_signal.R: plots the output of measure_signal
  • trim_adapters: based on Jason Buenrostro's utility for trimming Illumina adapters by aligning paired reads to each other.

A Python library you can use in your own tools for processing ATAC-seq data

The code underpinning our command-line tools has allowed us to make our pipelines shorter and faster. Our ATAC-seq scoring functions work directly with a BAM file and run in parallel, without the overhead of invoking external applications. Particularly if you're trying to produce quantitative metrics from your data, starting with your BAM files, converting them to BED and bigWig so you can run bigWigSummary, you might find your pipeline can be simplified too.

Requirements

  • Python. We've run it successfully under versions 2.7 and 3.5.
  • pyBigWig
  • pysam
  • python-levenshtein
  • sexpdata

Installation

At the command line:

git clone https://github.com/ParkerLab/atactk
pip install ./atactk

Or in one step, if you don't want a local copy:

pip install git+https://github.com/ParkerLab/atactk

Documentation

http://atactk.readthedocs.org/en/latest/

License

GPLv3 or any later version.