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Related Concept Videos

RNA-seq03:21

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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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Related Experiment Video

Updated: Oct 7, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms.

Xuemin Dong1,2, Shanshan Dong3, Shengkai Pan4

  • 1Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.

BMC Bioinformatics
|January 7, 2022
PubMed
Summary
This summary is machine-generated.

RNA-combine is a new open-source toolkit for analyzing transcriptome data from various sequencing platforms. This tool simplifies processing, analysis, and visualization for both bioinformaticians and non-bioinformaticians.

Keywords:
Non-bioinformaticianTranscriptomeUser-friendlyVisualization

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Transcriptome analysis is crucial for understanding cellular and organ function.
  • Existing tools often support only single sequencing platforms and limited analysis modules.
  • There is a need for an integrated, user-friendly toolkit for diverse transcriptome data.

Purpose of the Study:

  • To develop an open-source toolkit for comprehensive transcriptome data processing and analysis.
  • To provide a solution for both bioinformatician and non-bioinformatician users.
  • To enable visualization of analysis results from multiple sequencing platforms.

Main Methods:

  • Developed a Linux-based toolkit named RNA-combine.
  • Integrated modules for quality assessment, downstream analysis, and visualization.
  • Supported data from bulk RNA-seq (Illumina), single-cell RNA-seq (10x Genomics), and Iso-Seq (PacBio).

Main Results:

  • RNA-combine automates quality assessment and downstream analysis for diverse transcriptome data.
  • The toolkit includes over 10 analysis modules, exceeding other examined toolkits.
  • Results are visualized, facilitating interpretation.

Conclusions:

  • RNA-combine is a reliable tool for transcriptome data processing and interpretation.
  • The toolkit is suitable for both bioinformaticians and non-bioinformaticians.
  • Source code is available on GitHub for accessibility and further development.