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Tutorial RNASeq of comparative transcriptomics based on the species Sparus aurata

  1. Página Principal
  2. Nuestros cursos
  3. Tutorial RNASeq differential expression
  4. 2.2.2 - Quality analysis and preprocessing
◄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
    • 2.2. - MAPPING & COUNTING PROTOCOL
      • 2.2.1 - Preparing your experiment
      • 2.2.2 - Quality analysis and preprocessing
      • 2.2.3 - Mapping
      • 2.2.4 - Postprocessing
      • 2.2.5 - Differential Expression analysis
  • 3. PIPELINE MODE TUTORIAL
    • 3.1 - TopHat/Hisat2 & Cufflinks protocol
    • 3.2 - Mapping & Counting protocol
  • 4. BIBLIOGRAPHY
  • CITE US
  • 2.2.2 - Quality analysis and preprocessing


    The tools and analyses for data preprocessing are the same as those used during the Tophat/Hisat2 & Cufflinks protocol in Section 2.1.2 of this tutorial. This means that you do not need to repeat these analyses, just do the following:

    • Move the fastq files preprocessed with the Tophat/Hisat2 & Cufflinks protocol from the Tophat_cufflinks/02_preprocessing folder to the Mapping_counting/02_preprocessing folder because you will use these fastq files in the mapping step.


    • Move the fasta file with the fSpaAur1.1 reference transcriptome from your directory browser to the Mapping_counting/03_refseq. As previously said, the GTF file is not necessary.

    ◄2.2.1 - Prepare your experiment for the mapping & counting analysis2.2.3 - Mapping►
    • 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
      • 2.2. - MAPPING & COUNTING PROTOCOL
      • 2.2.1 - Prepare your experiment for the mapping & counting analysis
      • 2.2.2 - Quality analysis and preprocessing
      • 2.2.3 - Mapping
      • 2.2.4 - Postprocessing
      • 2.2.5 - Differential Expression analysis
      • 3. PIPELINE MODE TUTORIAL
      • 3.1 - TopHat/Hisat2 & Cufflinks protocol
      • 3.2 - Mapping & Counting protocol
      • 4. BIBLIOGRAPHY
      • Pipeline mode: Tophat & Cufflinks protocol results
      • Pipeline mode: Mapping & Counting protocol results
      • CITE US
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