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BBGProtocols
BBGProtocols
- BBGlab best practices on data organization
- Info for bbg-coffee drinkers
Cluster basics
Cluster basics
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- New folder in workspace
- Running notebooks in the cluster
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  Submitting jobs
  - Qmap Submit
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Datasets
Datasets
- BBG standards
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  - Variant consequences
- General datasets
  General datasets
  - BeatAML
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- Inhouse datasets
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- Other data
  Other data
IRB
IRB
- VPN
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- Fifteen wifi
Methods
Methods
- Sequencing
  Sequencing
  - Bedtools
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  - Cutadapt
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  - Trimmomatic
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  - pysam
  - Variant callers
    Variant callers
    
    HMFtools
    
    MosaicForecast
    
    Mutect2
    
    Platinum
    
    Sarek
  - singleCell
    singleCell
    
    ArchR: Processing scATAC sequencing data
    
    CellRanger
    
    Mosaic - python package
    
    Seurat
    
    Tapestri insights
    
    Tapestri pipeline
- Signature
  Signature
Plots and scripts
Plots and scripts
Tools
Tools
- Conda
- Docker
- GitHub Copilot
- McGyver
- Nextflow
- Snakemake
- BBG tools
  BBG tools
  - BGconfig BGconfig
    Table of contents
    
    Description
    
    Reference
  - BGdata
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  - BGpack
  - BgReference
  - BGsignature
  - BGvep
  - OpenVariant
- Programming
  Programming
  - Git
  - Python
    Python
    
    Updating package on pypi
- Singularity
  Singularity
- VSCode
  VSCode
  - VSCode from the bbg-cluster
  - VSCode in interactive node

Table of contents

Description
Reference

BGconfig¶

Description¶

Reference¶

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