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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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Updated: Jul 1, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

HaplotagLR: An efficient and configurable utility for haplotagging long reads.

Monica J Holmes¹, Babak Mahjour², Christopher P Castro¹

¹Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.

|March 13, 2024

Summary

This summary is machine-generated.

HaplotagLR is a new tool that improves haplotagging for genomic sequence analysis. It accurately assigns sequencing reads to parental haplotypes, enhancing understanding of genetic variation and disease risk.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Understanding genetic variant functional effects is key in genomics.
Millions of variants per genome influence traits and disease risk.
Neighboring variant interactions are vital for accurate functional effect prediction.

Purpose of the Study:

To introduce HaplotagLR, a user-friendly haplotagging tool for long sequencing reads.
To address limitations of existing haplotagging methods, such as error rate control.

Main Methods:

HaplotagLR utilizes a multinomial model and phased variant lists.
It is user-configurable and incorporates an error model for False Discovery Rate (FDR) control.

Main Results:

HaplotagLR outperforms leading haplotagging methods in simulated data, especially for specificity.
It demonstrates 7% greater sensitivity on real sequencing data.

Conclusions:

HaplotagLR enhances the utility of haplotagging for analyzing genetic variation.
The tool provides a foundation for future advancements in haplotagging methodologies.