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Related Experiment Video

Updated: May 23, 2025

ATAC-Seq Optimization for Cancer Epigenetics Research
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UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline.

Jordana Lindner1, Bareket Dassa1, Noa Wigoda1

  • 1Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, 76100, Rehovot, Israel.

BMC Bioinformatics
|March 7, 2025
PubMed
Summary
This summary is machine-generated.

UTAP2 simplifies complex transcriptome and epigenome data analysis for researchers. This open-source pipeline makes next-generation sequencing data accessible, even for those with limited bioinformatics expertise.

Keywords:
ATAC-seqBioinformatics workflowBulk MARS-SeqChIP-seqClusteringDifferential gene expressionEpigenomeGene expression profileGene-set enrichmentGenome mappingNGS (next-generation sequencing)NormalizationPeak callingRNA-SeqRNA-seqRibo-SeqSequence analysis pipelinesTranscriptomeUMI (unique molecular identifier)

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Next-generation sequencing (NGS) has revolutionized biological research by enabling comprehensive transcriptome and epigenome analysis.
  • Advances in sequencing technology offer high throughput at reduced costs, but data analysis still requires significant bioinformatics expertise.
  • Democratizing access to sequence analysis tools is essential for researchers to fully utilize NGS data.

Purpose of the Study:

  • To present UTAP2, an enhanced, user-friendly, open-source pipeline for transcriptome and epigenome data analysis.
  • To streamline the process from raw sequence data to annotated gene expression and genomic regions.
  • To empower researchers with limited bioinformatics skills to efficiently analyze complex sequencing data.

Main Methods:

  • UTAP2 is an open-source pipeline designed for analyzing transcriptome and epigenome data.
  • The pipeline handles data from raw sequences to gene/peak counts and differential analysis.
  • It provides organized results with plots, tables, and links for easy interpretation.

Main Results:

  • UTAP2 simplifies the analysis of gene expression and epigenetic modifications.
  • The pipeline generates organized reports with comprehensive data visualizations.
  • Previous version UTAP has been widely adopted and cited, indicating its utility.

Conclusions:

  • UTAP2 is available as an open-source installation for local servers and cloud platforms.
  • The pipeline can be installed using a single image, facilitating broad accessibility.
  • UTAP2 enables efficient, accurate, and reliable analysis of transcriptome and epigenome sequence data for researchers with varying bioinformatics expertise.