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VariantSeq: tutorial for usage with case study.
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VariantSeq Tutorial
01_FASTQC
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
01_FASTQC
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01_FASTQC
02_PRINSEQ
03_FASTQC
04_Bwa
05_picardAddReplaceReadGroups
06_picardMarkDuplicates
07_BQSR
08_mutect2
01_FASTQC
02_CUTADAPT
03_PRINSEQ
04_FASTQC
05_TOPHAT
06_CUFFLINKS
06_CUFFDIFF
01_FASTQC
02_CUTADAPT
03_PRINSEQ
04_FASTQC
05_TOPHAT
06_CUFFLINKS
06_CUFFDIFF
02_CUTADAPT
03_PRINSEQ
04_FASTQC
05_Bowtie2
06_CORSET
07_edgeR
01_FASTQC
02_CUTADAPT
03_PRINSEQ
04_FASTQC
05_Bowtie2
06_CORSET
07_edgeR
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Course sections
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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Valencia Lab
Parc Cientific Universitat de Valencia
Carrer del Catedràtic Agustín Escardino, 9. 46980 Paterna (Valencia) Spain
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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
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