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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. 2.1. - TOPHAT/HISAT2 & CUFFLINKS
◄2. STEP-BY-STEP MODE TUTORIAL3. PIPELINE MODE TUTORIAL►
  • 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
  • 2.1. - TOPHAT/HISAT2 & CUFFLINKS

    “Tophat/Hisat2 & Cufflinks” is recommended for RNA-seq studies when the reference genome has an annotation GTF/GFF file. To complete the tutorial for this protocol, you will need the 10 fastq files for the PVL group (samples from JVB-R1 to JVB-R10), the 5 fastq files for the control group (samples from JVB-R11 to JVB-R15), and the fasta file with the GRCh38.95 reference genome and the associated GTF file. 
    ◄2. STEP-BY-STEP MODE TUTORIAL2.1.1 - Preparing your experiment►
    • 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
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