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Next Generation Sequencing pipeline: a joint LONI – BIRN [UCLA – UCI] collaborative project

Next Generation Sequencing pipeline: a joint LONI – BIRN [UCLA – UCI] collaborative project. F. Macciardi – March 16, 2011. Pipeline: the concept from sequencing to interpretation of results. Wet lab. Wet lab. Molecular. Seq data production DNA, RNA, ChiP [all platforms].

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Next Generation Sequencing pipeline: a joint LONI – BIRN [UCLA – UCI] collaborative project

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  1. Next Generation Sequencing pipeline:a joint LONI – BIRN[UCLA – UCI]collaborative project F. Macciardi – March 16, 2011

  2. Pipeline: the conceptfrom sequencing to interpretation of results Wet lab Wet lab Molecular Seq data production DNA, RNA, ChiP [all platforms] Seq data production DNA, RNA, ChiP [all platforms] Dry lab 1 Dry lab 2 Dry lab 3 Sys bio Data Analysis 1 QC Coverage Callability …. Data Analysis 2 Visualization SNP calls CNV / indels specific motifs Data Analysis 1st level results interpretation Bioinformatics 1st level results interpretation & modeling LONI - BIRN pipeline proposal Step 1 Step 2

  3. NGS Pipeline: general plan Bioinformatics / Dry Lab 1 & 2 - Step 1 SNPs Alignment & Assembly * QC, Data Cleaning .BAM Visualization CNVs DNA motifs Signatures • Workflow 1 Workflow 2 (in progress) Workflow 3 Workflow 4 …

  4. LONI - BIRN PIPELINE Implementation of Genomics and Informatics Pipeline Protocols • protocol design • tool installation • module definition • workflow implementation • workflow validation, and dissemination

  5. NGS Pipeline workflow 1: Alignment and Assembly

  6. NGS Pipeline editing & redesign

  7. NGS Pipeline: QC control (in progress)

  8. LONI - BIRN PIPELINE Wiki

  9. LONI - BIRN PIPELINE paper in writing to be submitted soon …

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