sRNAplot

Purpose

A tool to visualize various small RNA characteristics

Requirements

Written in python3.

Requires:

WebLogo 3 - NOTE: please install weblogo rather than seqlogo

signature.py by Christophe Antoniewski - to install, simply copy the signature.py file (above) into your ~/bin/ directory (NOTE: it must be installed in this directory).

Usage

Basic usage is:

sRNAplot.py -s samplename -i input.bam

sRNAplot accepts the following additional arguments (all of which have defaults already set):

-m (minimum sRNA length, default=17)

-M (maximum sRNA length, default=35)

--seqlogo (plot separate seqlogos for sense and antisense sRNAs)

--pingpong (plot Ping-Pong overlap signature)

--distribution (plot sRNA length distribution)

--unique (plot unique reads only i.e. collapse identical reads)

-h (display help message)