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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
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SCRAM: a pipeline for fast index-free small RNA read alignment and visualization
Stephen J Fletcher1,2, Mikael Boden1, Neena Mitter2
1School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
Bioinformatics (Oxford, England)
|March 20, 2018
Summary
SCRAM is a new tool for analyzing small RNA data, aiding in understanding gene regulation and genome stability. This Small Complementary RNA Mapper simplifies exploring crucial small RNA datasets.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Small RNAs are vital for gene regulation, viral defense, and genome stability.
- Numerous aspects of small RNA biogenesis and function require further investigation.
Purpose of the Study:
- To introduce SCRAM (Small Complementary RNA Mapper), a novel tool for small RNA data analysis.
- To enhance the exploration and visualization of small RNA sequencing datasets.
Main Methods:
- Development of a user-friendly short read aligner and visualization suite.
- Implementation of the SCRAM pipeline using Go and Python.
Main Results:
- SCRAM provides an enhanced approach to exploring small RNA datasets.
- The tool facilitates deeper insights into small RNA functions and biogenesis.
Conclusions:
- SCRAM offers a valuable resource for researchers studying small RNA biology.
- The freely available pipeline supports advancements in gene regulation and genome stability research.
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