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VariantSeq: tutorial for usage with case study.

  1. Página Principal
  2. Nuestros cursos
  3. VariantSeq Tutorial
  4. 2.3 - Mapping
◄2. STEP-BY-STEP MODE TUTORIAL4. BIBLIOGRAPHY►
  • 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 VariantSeq and the Server-Side
  • 2. STEP-BY-STEP MODE TUTORIAL
    • 2.1 - Preparing your experiment
    • 2.2 - Quality analysis and preprocessing
    • 2.3 - Mapping
    • 2.4 - Postprocessing
    • 2.5 - Variant calling
    • 2.6 - Variant filtering
    • 2.7 - Annotation
  • 3. PIPELINE MODE TUTORIAL
  • 4. BIBLIOGRAPHY
  • CITE US
  • 2.3 - Mapping


    The goal of mapping is to align the reads of each fastq library to the respective regions of the reference genome where the reads likely originated. Mapping the reads to the reference genome typically involves the alignment of millions of short reads to the genome using algorithms for fast alignment implemented using mapper tools.

    To complete mapping with the SNP/Indel protocol, we map the preprocessed fastq files on the hg19 reference. The Step-by-Step menu offers you two DNAseq mappers: Bowtie2 (Langmead and Salzberg 2012) and BWA (Li and Durbin 2009). In this tutorial we will use BWA because is the typical mapper for exome analysis. To this end, please go to the Step-by-Step menu path, SNP/Indels → Mapping → DNAseq mappers → BWA and proceed as indicated in Video 4


                                   Video 4. Mapping fastq libraries on the hg19 genome with the BWA implementation of VariantSeq.

    Expected results from mapping analysis

    When BWA is complete, you will receive a bam file per sample with the reads mapped against the reference genome.  

    The expected results of this step are available in the following link Mapping

    Remember you can check how the job was completed by accessing the job tracking panel. Pay particular focus on the log file metrics showing the % or reads successfully mapped. An acceptable value is more than 80% of reads mapped per fastq library. If the % is lower than 70% try to preprocess the samples again for better cleaning of the fastq libraries.  

    To learn more about BWA see, http://bio-bwa.sourceforge.net

    ◄2.2 - Quality analysis and preprocessing2.4 - Postprocessing►
    • 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 Variantseq and the Server-Side
      • 2. STEP-BY-STEP MODE TUTORIAL
      • 2.1 - Preparing your experiment
      • 2.2 - Quality analysis and preprocessing
      • 2.3 - Mapping
      • 2.4 - Postprocessing
      • 2.5 - Variant calling
      • 2.6 - Variant filtering
      • 2.7 - Annotation
      • 3. PIPELINE MODE TUTORIAL
      • 4. BIBLIOGRAPHY
      • Pipeline mode: SNP/Indels results
      • CITE US
      • 4. BIBLIOGRAPHY
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