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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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CLIPSeqTools--a novel bioinformatics CLIP-seq analysis suite.

Manolis Maragkakis¹, Panagiotis Alexiou¹, Tadashi Nakaya²

¹Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

RNA (New York, N.Y.)

|November 19, 2015

Summary

This summary is machine-generated.

This study introduces CLIPSeqTools, a flexible computational suite for analyzing RNA binding protein (RBP) HITS-CLIP sequencing data. CLIPSeqTools simplifies RBP target identification from raw sequencing data with minimal user input.

Keywords:

Argonaute CLIP-seq HITS-CLIP RNA binding protein miRNA

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Published on: October 5, 2018

Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

High-throughput sequencing methods like HITS-CLIP (UV crosslinking, immunoprecipitation, and sequencing) are crucial for identifying RNA targets and binding sites of RNA binding proteins (RBPs).
Current CLIP-seq data analysis workflows are diverse and highly dependent on the specific RBP, highlighting the need for adaptable and efficient computational tools.

Purpose of the Study:

To develop and present CLIPSeqTools, a novel, flexible computational suite designed for comprehensive analysis of CLIP-seq data.
To enable in-depth analysis of CLIP-seq datasets from raw sequencing reads to biological insights with minimal user intervention.

Main Methods:

Development of CLIPSeqTools, a computational suite offering a range of tools for CLIP-seq data analysis.
Utilizing CLIPSeqTools to analyze Ago-miRNA HITS-CLIP datasets generated from human brain samples.

Main Results:

CLIPSeqTools provides a flexible and efficient platform for analyzing raw CLIP-seq data.
The suite supports extensive customization, facilitating in-depth analysis and adaptability to various CLIP-seq experimental designs.

Conclusions:

CLIPSeqTools offers a powerful and user-friendly solution for the analysis of CLIP-seq data, addressing the limitations of existing diverse approaches.
The demonstrated application on Ago-miRNA HITS-CLIP data from human brains showcases the suite's capability in identifying RBP targets and binding sites.