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Related Concept Videos

RNA-seq03:21

RNA-seq

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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. 
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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Related Experiment Video

Updated: Nov 12, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
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WASP: a versatile, web-accessible single cell RNA-Seq processing platform.

Andreas Hoek1, Katharina Maibach2,3, Ebru Özmen2

  • 1Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany. andreas.hoek@computational.bio.uni-giessen.de.

BMC Genomics
|March 19, 2021
PubMed
Summary
This summary is machine-generated.

WASP is a new, free software tool that simplifies processing and analyzing single-cell RNA sequencing (scRNA-seq) data. It offers intuitive pre- and post-processing for Drop-Seq, ddSEQ, and 10x Genomics data, aiding biological research.

Keywords:
10xBarcodeR shinyRNA-SeqSingle cellSnakemakeUMIddSEQ

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Single-cell RNA sequencing (scRNA-seq) is a powerful technology for analyzing cellular heterogeneity and identifying cell populations.
  • Its application spans diverse areas of medical and biological research, offering unprecedented biological insights.
  • However, scRNA-seq data analysis requires advanced bioinformatic expertise, posing a challenge for many researchers.

Purpose of the Study:

  • To present WASP, a novel software solution designed for the efficient processing and analysis of scRNA-seq data.
  • To provide an intuitive and user-friendly tool that simplifies complex bioinformatic workflows.
  • To enable researchers to readily explore cellular heterogeneity and gene expression patterns.

Main Methods:

  • WASP utilizes a Snakemake workflow for the initial processing of raw sequencing reads (Drop-Seq, ddSEQ, 10x Genomics).
  • It generates demultiplexed gene expression matrices with integrated quality metrics.
  • An accompanying R Shiny application facilitates interactive visualization and comprehensive downstream analysis, including differential gene expression and clustering.

Main Results:

  • WASP successfully processes raw scRNA-seq reads and generates gene expression matrices.
  • The software provides quality metrics and supports differential gene expression analysis and cell population clustering.
  • The R Shiny application allows for interactive exploration of results, compatible with WASP-generated or external data.

Conclusions:

  • WASP offers an intuitive, easy-to-use, and freely available software package for scRNA-seq data processing and exploration.
  • It uniquely combines pre- and post-processing capabilities for ddSEQ and 10x Genomics data.
  • WASP's modular design, Docker containerization, and standalone options enhance accessibility for researchers across different technical backgrounds.