Tamaño de fuente
  • A-
  • A
  • A+
Color del sitio
  • R
  • A
  • A
  • A
eCampus
  • INICIO
  • eCAMPUS
    AULA
  • FORO
  • English ‎(en)‎ Español - Internacional ‎(es)‎
  • Acceder
Salta al contenido principal

Tutorial RNASeq for detection of pre-tumoral biomarkers using a group case study of Proliferative Verrucous Leukoplakia

  1. Página Principal
  2. Nuestros cursos
  3. RNASeq Leukoplakia
  4. 3.1 - TopHat/Hisat2 & Cufflinks protocol
◄3. PIPELINE MODE TUTORIAL4. ACKNOWLEDGEMENTS►
  • CONTENTS
  • 1. PRELIMINARY INFORMATION
    • 1.1 - Tutorial objective
    • 1.2 - Tutorial material and case study
    • 1.3 - Experiment design and support
    • 1.4 - Installing and activating RNASeq and the Server-Side
  • 2. STEP-BY-STEP MODE TUTORIAL
    • 2.1. - TOPHAT/HISAT2 & CUFFLINKS
      • 2.1.1 - Preparing your experiment
      • 2.1.2 - Quality analysis and preprocessing
      • 2.1.3 - Mapping
      • 2.1.4 - Transcriptome Assembly
      • 2.1.5 - Differential Expression analysis
      • 2.1.6 - GOSeq
  • 3. PIPELINE MODE TUTORIAL
    • 3.1 - TopHat/Hisat2 & Cufflinks protocol
  • 4. ACKNOWLEDGEMENTS
  • 5. BIBLIOGRAPHY
  • CITE US
  • 3.1 - TopHat/Hisat2 & Cufflinks protocol


    To complete this protocol using the pipeline mode, remember that you will need the following material:

    • The 10 fastq files for the PVL group (From JVB-R1 to JVB-R10)
    • The 5 fastq files for the control group (From JVB-R11 to JVB-R15)
    • The fasta file with the GRCh38.95 reference genome and its associated GTF file.
    • When you have this material ready, you can access the pipeline designer interface (RNAseq Protocols → Pipeline mode) and proceed as indicated in video 9


                                    Video 9. Tophat/Hisat2 & Cufflinks protocol for differential expression analysis executed using pipeline mode of RNASeq.

      Expected results from the Tophat/Hisat2 & Cufflinks protocol using the Pipeline execution mode:

      When the pipeline mode is complete, you will receive the results of differential expression sample with the reads mapped against the reference genome.

      The expected results of this step are available in the following link Pipeline mode: Tophat/Hisat2 & Cufflinks protocol

      Remember you can check if the job was successfully completed by accessing the job tracking panel of RNASeq. 

      To learn more about any tool used in the pipeline and their outputs see their respective manuals, referred in previous sections of this tutorial.

    ◄3. PIPELINE MODE TUTORIAL4. ACKNOWLEDGEMENTS►
    • Página Principal
    • Calendario
    • Secciones del curso
      • CONTENTS
      • 1. PRELIMINARY INFORMATION
      • 1.1 - Tutorial objective
      • 1.2 - Tutorial material and case study
      • 1.3 - Experiment design and support
      • 1.4 - Installing and activating RNASeq and the Server-Side
      • 2. STEP-BY-STEP MODE TUTORIAL
      • 2.1. - TOPHAT/HISAT2 & CUFFLINKS
      • 2.1.1 - Preparing your experiment
      • 2.1.2 - Quality analysis and preprocessing
      • 2.1.3 - Mapping
      • 2.1.4 - Transcriptome Assembly
      • 2.1.5 - Differential Expression analysis
      • 2.1.6 - GOSeq
      • 3. PIPELINE MODE TUTORIAL
      • 3.1 - TopHat/Hisat2 & Cufflinks protocol
      • 4. ACKNOWLEDGEMENTS
      • Pipeline mode: Tophat & Cufflinks protocol results
      • 5. BIBLIOGRAPHY
      • CITE US
    Configuraciones de accesibilidad
    About us
    Team
    Publications
    R&D
    Patents & trademarks
    Announcements
    Careers
    Journal Sequencing Partners

    Biotechvana


    Valencia Lab
    Parc Cientific Universitat de Valencia
    Carrer del Catedràtic Agustín Escardino, 9. 46980 Paterna (Valencia) Spain
    Madrid Lab
    Parque Científico de Madrid
    Campus de Cantoblanco
    Calle Faraday 7, 28049 Madrid Spain
    Contact us
    Phone: +34 960 06 74 93
    Email: biotechvana@biotechvana.com

    Esta plataforma forma parte de: IVACE PROJECT IMDIGB/2020/56


    Projectes de Digitalizació de PIME (DIGITALIZA-CV TELETREBALL)2020
    IVACE PROJECT IMDIGB/2020/56

    Biotechvana © 2021
    eCampus Privacy policy    eCampus Terms of use