Welcome to PolTools!

PolTools is a collection of bioinformatic programs analyzing PRO-Seq, PRO-Cap, and similar next generation sequencing experiments analyzing nascent RNAs.

It is primary written in python3, but utilizes R for plotting and C++ for computationally expensive analyses. These tools were developed in the Price Lab

Installation

Two options are provided for installation. Both assume you already have R and bedtools installed. If you do not have R installed, please install it as described here. If you do not have bedtools installed, please install it as described in the documentation

1. Install using pip and PyPI

$ pip3 install PolTools
$ source /etc/bash_completion.d/PolTools-completion.bash
$ PolTools build

2. Install from the github source

$ git clone https://github.com/GeoffSCollins/PolTools.git
$ sudo python3 PolTools/setup.py install
$ source /etc/bash_completion.d/PolTools-completion.bash
$ PolTools build

Table of Contents

• TES Fold Change Heatmap
• TES Heatmap
• Base Distribution
• Gene Body Fold Change Heatmap
• Gene Body Heatmap
• Make Regions File Centered on Max TSS
• Metaplot
• Multicoverage
• Nucleotide Heatmap
• Pausing Distance Distribution from Max TSS
• Read Through Transcription
• Region Fold Change Heatmap
• Region Heatmap
• Sequence from Around Max TSS
• Sequence Searches
• TPS Distance Per Gene
• Track Links From Bigwigs
• truQuant
• tsrFinder
• tsrPicker