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Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.

Florian Heyl¹, Daniel Maticzka¹, Michael Uhl¹

¹Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.

|November 12, 2020

Summary

This summary is machine-generated.

CLIP-Explorer is a new data analysis pipeline for RNA-binding protein targets. It supports various CLIP-Seq protocols and improves peak calling, crucial for understanding gene regulation.

Keywords:

CLIP-Seq Galaxy RNA data analysis protein

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Post-transcriptional regulation by RNA-binding proteins is crucial but not fully understood.
Cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-Seq) identifies RNA-binding protein targets.
The surge in CLIP-Seq data necessitates automated analysis pipelines for diverse experimental setups.

Purpose of the Study:

To develop a flexible and reproducible CLIP-Seq data analysis pipeline.
To accommodate various CLIP-Seq protocols including iCLIP, eCLIP, FLASH, and uvCLAP.
To address challenges in peak calling for accurate identification of binding sites.

Main Methods:

Development of the CLIP-Explorer analysis pipeline.
Adaptation of individual analysis steps, including peak calling, for different experimental settings.
Validation of CLIP-Explorer using eCLIP data and comparison with existing databases.

Main Results:

CLIP-Explorer supports multiple CLIP-Seq protocols (iCLIP, eCLIP, FLASH, uvCLAP).
Identified similar or novel sequence motifs for RNA-binding proteins like PTBP1 and U2AF2.
Optimized peak calling and provided recommendations for different experimental setups.

Conclusions:

CLIP-Explorer meets the need for a flexible pipeline for modern CLIP-Seq protocols.
Highlights limitations of current peak-calling algorithms and emphasizes robust peak detection.
Facilitates deeper understanding of RNA-binding protein functions and regulatory mechanisms.