PyMaSC

Python implemented MaSC algorithm for accurate mean fragment length estimation and quality control for ChIP-Seq.

Installation

PyMaSC is available as a Python package. Recommended Python versions are 2.7 or >=3.5.

1. Install numpy and pysam==0.15.1 before PyMaSC installation.
   

   pip install numpy pysam==0.15.1

   If you want to built with Cython native compiled sources, install cython additionally.
2. Install pymasc.

   pip install pymasc

   If Cython is not installed, pre-compiled C sources will be used.
3. pymasc, pymasc-plot and pymasc-precalc commands will be installed.

Download Mappability Tracks

Here we share the mappability tracks (bigwig format) for the human genome references, hg19, hs37d5 and hg38. Choose the track for a k-mer length which suits your sequence read length. Raw GEM mappability files and GEM indexes are available at here.

• GEM index for hg19 (4.01 GiB)
• GEM index for hs37d5 (4.05 GiB)
• GEM index for hg38 (4.25 GiB)

Tutorial

WIP