TheFraserLab / ASEr

Get ASE counts from BAMs or raw fastq data -- repackage of pipeline by Carlo Artieri
MIT License
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ASEr

.. image:: https://travis-ci.org/TheFraserLab/ASEr.svg?branch=master

Get ASE counts from BAMs or raw fastq data -- repackage of pipeline by Carlo Artieri

Scripts: MaskReferencefromBED.pl, create_individual_snp_files, CountSNPASE.py, create_phased_bed, GetGeneASE.py

Required software installed in PATH:

Required python libraries:

.. contents:: Contents

Installation

Simple install procedure::

git clone https://github.com/TheFraserLab/ASEr.git
cd ASEr
python ./setup.py install

Alternatively, to install without root privileges::

python ./setup.py install --user

Pipeline Flow


create_individual_snp_files



CountSNPASE


Note: this script has a multiplexing mode that can dramatically accelerate its performance by splitting sam/bam files and running in parallel on all the fragments. This mode will can be enabled with the -m multi argument. On a simple system it will just use threads up to a maximum of --threads. On a system with torque or slurm, it will submit its jobs to those systems. The cluster system is auto-detected, but you will need to provide the queue/partition to run in and other submission variables.


create_phased_bed



GetGeneASE