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Sequencing of mRNA from Whole Blood using Nanopore Sequencing
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Sequencing of mRNA from Whole Blood using Nanopore Sequencing

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Nanopore RNA Sequencing Analysis.

Tommaso Leonardi1, Adrien Leger2

  • 1Center for Genomic Science, Istituto Italiano di Tecnologia, Milano, Italy. tommaso.leonardi@iit.it.

Methods in Molecular Biology (Clifton, N.J.)
|April 9, 2021
PubMed
Summary
This summary is machine-generated.

Nanopore sequencing enables full-length RNA and cDNA analysis, presenting computational challenges. This guide details processing raw data into count tables for downstream applications using dedicated pipelines.

Keywords:
BioinformaticsDirect RNA sequencingNanoporeTranscriptomicscDNA sequencing

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Nanopore sequencing technology allows for the analysis of full-length RNA or cDNA molecules.
  • This novel data type presents unique computational challenges requiring specialized software and analysis pipelines.

Purpose of the Study:

  • To provide a comprehensive guide for processing raw Nanopore sequencing data.
  • To transform raw direct RNA sequencing (RNA-Seq) and cDNA sequencing (cDNA-Seq) data into a usable count table for downstream analyses.

Main Methods:

  • Conversion of raw direct RNA-Seq and cDNA-Seq data into FASTQ format.
  • Implementation of quality control and filtering steps for long reads.
  • Mapping of filtered long reads to a reference transcriptome or genome.

Main Results:

  • A clear workflow for processing Nanopore sequencing data is presented.
  • The described methods enable the generation of count tables essential for further biological interpretation.
  • Successful mapping of long reads to reference sequences is achievable with the outlined procedures.

Conclusions:

  • The chapter offers a practical guide to navigating the computational aspects of Nanopore sequencing data analysis.
  • This facilitates the use of full-length RNA and cDNA sequencing data in various biological research areas.
  • The presented pipeline addresses the need for robust analysis of long-read sequencing data.