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Related Experiment Video

Updated: Feb 11, 2026

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

Published on: February 13, 2013

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.

Nadia M Davidson^1,2, Alicia Oshlack^1,2

¹Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia.

|May 4, 2018

Summary

This summary is machine-generated.

Necklace is a new software pipeline that integrates genome-guided and de novo assembly with reference annotations. This creates a comprehensive superTranscriptome for improved RNA sequencing analyses and differential expression testing.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

RNA sequencing (RNA-seq) analysis benefits from genome-guided and de novo assembly, especially with incomplete reference genomes or annotations.
Existing tools lack methods for integrating assembled transcriptomes with reference annotations.

Purpose of the Study:

To develop a software pipeline for integrating assembled transcriptomes with reference genome annotations.
To create a comprehensive superTranscriptome for enhanced RNA-seq analysis.

Main Methods:

The Necklace pipeline performs genome-guided and de novo assembly.
It combines assembled transcriptomes with reference genome annotations.
It constructs a superTranscriptome and aligns RNA-seq reads for differential expression testing.

Main Results:

Necklace generates a more comprehensive transcriptome by combining assembled and annotated transcripts.
This approach benefits the majority of organisms, especially those with incomplete genomic data.
RNA-seq data can be mapped to the superTranscript for standard differential expression testing.

Conclusions:

Necklace enables the construction of a comprehensive transcriptome from assembled and annotated data.
This leads to improved RNA-seq analysis and differential expression testing.
The pipeline provides a valuable tool for transcriptomic studies with incomplete reference genomes.