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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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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Librarian: A quality control tool to analyse sequencing library compositions.

Kartavya Vashishtha¹, Caroline Gaud², Simon Andrews²

¹Independent Researcher, New Delhi, India.

|January 26, 2024

Summary

DNA sequencing library preparation methods create distinct nucleobase composition profiles. Analyzing these profiles helps identify library types and potential technical biases in sequencing data quality control.

Keywords:

FastQ base composition high throughput sequencing quality control sequencing libraries

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Robust DNA sequencing data analysis requires quality control to minimize technical bias.
Nucleobase frequency at each position across sequencing reads is an easily obtainable metric.
This study investigates nucleobase composition differences across standard DNA library preparation methods.

Purpose of the Study:

To characterize nucleobase composition profiles of different DNA library types.
To develop a method for estimating library type based on composition.
To introduce a tool for quality assurance in DNA sequencing.

Main Methods:

Analysis of nearly 3000 publicly available DNA sequencing datasets.
Application of Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction.
Comparison of test library compositions against established profiles.

Main Results:

Most DNA library types exhibit unique nucleobase composition profiles.
A method was developed to estimate the resemblance of a test library to known types.
The Librarian tool was created for checking base compositions against known library types.

Conclusions:

Library preparation significantly impacts per-position nucleobase content.
Comparing test libraries to a database of known types allows prediction of preparation methods.
The Librarian tool aids in early detection of potential irregularities for quality assurance.