stepRNA 1.1b0

Align short RNA seqeuncing reads to determine the length of of overhang.

stepRNA

Overview

stepRNA is a RNA-seq read processor, based on bowtie2, that will align small RNA-seq query reads (passenger sequences) to reference sequences (siRNAs) and output information about the type and length of overhangs uncovered. It was originally developed for uncovering Dicer processing signatures but is not limited to just this.

Table of Contents:

• Installation
• Use
• Example
• News
• Licence
• Additional Information

Installation

In order for stepRNA to run you must have:

• Bowtie2 >= v2.3.4 (see BOWTIE2 website for more details)
• Bio >= v0.3.0 (automatically installed with pip)
• numpy >= v1.20.1 (autoamtically installed with pip)
• pysam >= v0.16.0.1 (autoamtically installed with pip)

To install with pip:

pip install stepRNA

To install from source:

1. Download stepRNA-X.X.X.tar.gz from PyPI_URL:
2. Unzip it:

tar -xvzf stepRNA-X.X.X.tar.gz

3. Move into stepRNA-X.X.X repository:

cd stepRNA-X.X.X

4. Run the installation:

pip install .

Installing into a Virtual Environment

This can be useful if root privalages are not available to the user.

1. Create a virutal environment:

We recommend using virtualenv pip install virtualenv

2. Create and activate the environment:

virtualenv stepRNA_env

source /stepRNA_env/bin/activate

3. Install with pip:

pip install stepRNA

Alternative:

Download the GitHub repository then make the script executable with: chmod +x bin/stepRNA

Then either:

• Make a symbolic link for stepRNA.py to your bin directory ln FULL_PATH_TO_stepRNA.py FULL_PATH_TO_BIN
• Direct PATH to the directory with stepRNA in it export PATH=$PATH:FULL_PATH_TO_GitHubRepo

Use:

See the documentation for a detailed description on how to use stepRNA (MANUAL)

The quickest way to use stepRNA:

stepRNA --reference REFERENCE --reads QUERY

This will align the reads to the reference sequences and output into the current diretory using the READS filename as the prefix. REFERENCE and QUERY must have unique FASTA headers (if not use -u)

Helpful options:

• --name can be used to customise the prefix name
• --directory can be used to specify an output directory

Example:

Using the reads from stepRNA/example_data:

stepRNA --reference stepRNA/example_data/FILENAME -- reads stepRNA/example_data/FILENAME --directory stepRNA_example

This will create a new direxotry called stepRNA_example that contains:

• AligmentFile/; a directory containing BAM files for each of the overhang lengths
• CSVs; containing count information (see MANUAL for more information)

News

Latest release notes:

Version 1.0.0 - 25 Feb, 2020

• First public release (v1.0.0)
• Caveats: Manual is still incomplete, untested on Windows
• Features such as log file outputs still to be finalised

See NEWS for historical updates of release notes

Licence

stepRNA is licensed under the MIT license. See LICENSE file for details.

Additional Information

For more information:

• Go to FAQs to see commonly asked quesitons
• Loo at the USER MANUAL to see detailed instructions and all of the available options

If you use stepRNA in your work please cite:

stepRNA: identification of Dicer-processing signatures and passenger strand lengths in small RNA (Murcott, Pawluk & Hunt, 2021)