sRNAanalyst

A Comprehensive Tool for In-depth Analysis of sRNA-seq Data across Conditions and Target Genes.

Main Features

1. Universal Preprocessing Tool

• Provides a versatile preprocessing tool that seamlessly integrates with various utilities such as Cutadapt and Bowtie, enabling the construction of customized preprocessing workflows.

2. Downstream Analysis Tool

• Facilitates transcriptome-wide examination of NGS sequences under specific gene lists using several downstream analysis tools.

Note

This version incorporates numerous improvements in performance and architecture, including the addition of a new preprocessing workflow. For information on the previous version and related research paper, please refer to the RDT project.

Downstream Tools

1. Density Distribution: Enables observation of distribution across different regions, facilitating the comparative analysis of results across different conditions and target genes.
   

2. Metagene Distribution: Allows the overlay of target genes for an overview of their collective distribution patterns.
   

3. Position Distribution: Facilitates observation of distribution around specific positions, currently including boundaries and start/stop codons.

4. Fold-change Plot: Permits the examination of the magnitude of changes between two conditions within different regions.
   

5. Scatter Plot: Enables the observation of the relative distribution of two conditions within different regions.
   

Getting Start

# download this project
git clone https://github.com/RyanCCJ/sRNAanalyst.git
cd sRNAanalyst

# an example of worm (C.elegans) 22G-RNAs is provided
cd example/script/

# perform preprocessing and generate various intermediate files
sh 22G_preprocess.sh

# perform downstream analysis and generate various analysis graphics
sh 22G_analyze.sh

It is recommended to independently compose a suitable workflow for applying preprocessing tool and to use or import the analysis tool accordingly. The two main programs are located in the src/ directory, namely srna_preprocess.py and srna_analysis.py. The analysis tool will additionally require two additional modules: utility.py and computation.py. For detailed usage instructions, please refer to the doc.

Note

The examples in this project require approximately 530MB of disk space. Please ensure you have sufficient space for operations. Alternatively, you can download only the source code and configuration files.

Web Tool

If you prefer a quick trial, you can explore our web tool.

1. Preprocess Page:

• Provides a user-friendly workflow for customizing preprocessing steps.
• Users can utilize our universal tool to achieve specific effects.

2. Analysis Page:

• Integrates various downstream analysis tools.
• Users can input experimental or literature data, or selectively input a target list of interest for further analysis.

3. Database Page:

• Includes literature data such as NGS raw-read, reference, and a portion of the nematode target list for reference.

Note

All uploaded data and analysis results will be retained for only 3 days. Please make sure to record your job ID. If you have additional requirements, consider exploring our Docker version.

Documentation

To see full documentation, please check this project's wiki.

Requirements

Running sRNAanalyst require Linux or MacOS. Other Unix environments will probably work but have not been tested. Windows users can use Windows Subsystem for Linux.

• Python >= 3.5
• numpy >= 1.12
• seaborn >= 0.9, < 0.12
• matplotlib >= 2.2
• pandas >= 0.23, < 2.0
• pysam >= 0.20
• scipy >= 1.1
• tqdm >= 4.0
• oyaml >= 1.0
• cutadapt >= 2.10
• rpy2 >= 3.0.5

EdgeR statistical test

• R >= 4.3
• BiocManager >= 1.30.22
• edgeR >= 4.0.2

Box-plot statistical test

If Python >= 3.6

• statannotations >= 0.6.0

If Python >= 3.5, < 3.6

• statannot = 0.2.3

Important

There are some bugs in the statannot package. Before usage, please refer to the doc for more details.

LICENSE

Please refer to our MIT license.