BCU Bulk Pipeline Documentation

Bulk high throughput sequencing datasets (RNA-Seq / ATAC-Seq / ChIP-Seq) are processed via in-house software pipelines.

Other Manuals:

For Single-cell analyses please consult: BCU SC Manual	For BCU Repository please consult: BCU Repository Manual

Table of Contents

Manual

• Overview
• Quickstart Analysis
  • Workflow
  • Output Files
  • Common Issues
• Analysis: XLSX
  • Sheet Overview: Statistics
  • Sheet Bigmatrix: Counts Per Feature + Contrasts
  • Sheet GSO: Non-Directional Gene Set Overrepresentation with Kobas
  • Sheet GSO_BAR: Directional Gene Set Overrepresentation with Kobas
  • Sheet GSEA: Gene Set Enrichment with fGSEA
• Analysis: PPTX
  • Fixed Header Slides
  • Methods
  • Read Classification
  • Sample Correlation: Scatter
  • Sample Correlation: Top50 Genes
  • Sample Correlation: Global Heatmaps
  • Sample Correlation: PCA
  • UpSetR
  • Volcano / MA
  • Heatmaps: DEGs
  • Gene Set Overrepresentation
• FAQ
  • Questions
    • Gene set enrichment?
  • IGV - offline
  • IGV - online
  • Outlier Samples
  • Batch Correction
  • DEG Cutoffs
  • Peak Calling
  • Reference Genome
  • Multi-Mapping Reads
  • Deduplication
  • Mitochondria and Ribosomes
  • HTML Plots
  • GSO: Kobas
  • GSEA: fGSEA
  • TFBS: PSCAN
  • TFBS: TOBIAS
  • TFBS Per Gene: MOODS
  • Nucleosome Positioning: Nucleodetective
  • Visualization: Wilson
  • Deeptools Coverage Plot
  • Complex Heatmap
  • Enriched Heatmap
  • Scatter Plot
  • Sashimi Plot
  • Web: StringDB
  • Web: Metascape
• Terminology / Tests
• Links
• Contact
• TODO

Administration / Development

• Administration / Development
  • Changelog
  • Developer Links
  • Bulk Pipelines: How to run
  • RNA-Seq
    • RNA-Seq: Config Files
    • RNA-Seq: Commandline Syntax
  • ATAC/ChIP-Seq
    • ATAC/ChIP-Seq: Config Files
    • ATAC/ChIP-Seq: Commandline Syntax
  • Output folder structure
  • Report
  • FAQ Admin
    • Admin: GEO submission
    • Admin: Combined Upload/Deploy
    • Admin: Transfer to S3
    • Admin: Deploy IGV container
    • Admin: Create Report Email
    • Admin: Deploy Wilson container
    • Admin: Deeptools Coverage
    • Admin: TFBS Analyses per gene: MOODS
    • Admin: Find homologous genes
    • Admin: Join/concat/expand files
  • DOC Syntax Examples
    • sub headline