1. BD Rhapsody™ Sequence Analysis Pipeline
  2. Setup and Running Guide
    ❱
    1. Input Files and Parameters
      ❱
      1. FASTQ files
      2. Reference Files
      3. Pipeline Parameters
    2. Seven Bridges Setup
      ❱
      1. Seven Bridges Account
      2. Create a New Project
      3. Upload FASTQ Files
      4. Upload Reference Files
      5. Import the Pipeline App
      6. Create Task and Run the Pipeline
      7. Download the Output
    3. Local Server Setup
      ❱
      1. System and Software Installation
      2. Input Specification File
      3. Run the Pipeline with CWL-runner
  3. Pipeline Steps and Algorithms
    ❱
    1. Read Quality Filter
    2. Annotate R1 Cell Label and UMI
    3. Align and Annotate R2 Reads
    4. Valid Read Pairs
    5. Molecules and Error Correction
    6. Determine Putative Cells
    7. Sample Tag Analysis
    8. Generate Expression Matrix Datatables
    9. Annotate BAM
    10. TCR and BCR Analysis
    11. ATAC-Seq Analysis
  4. Output Files
    ❱
    1. Metrics Summary CSV
    2. Pipeline Report HTML
    3. Cell-by-Feature Data Tables
    4. BAM and BAM Index
    5. Single-cell Analysis Tool Inputs
    6. Bioproduct Statistics
    7. Gene Biotype Counts
    8. Sample Tag Metrics
    9. Sample Tag Calls
    10. Sample Tag Folders
    11. VDJ Metrics
    12. VDJ Per Cell
    13. VDJ Contigs AIRR
    14. Protein Aggregates Experimental
    15. Immune Cell Classification
    16. Dimensionality Reduction
    17. ATAC Fragments
    18. ATAC Transposase Sites
    19. ATAC Peaks
    20. ATAC Peak Annotation
    21. ATAC Data Tables
    22. ATAC Metrics
  5. Troubleshooting Guide
    ❱
    1. Access Log Files
    2. Output Metrics and Associated Problems
    3. Skim Sequencing for Assessing Library Quality
  6. Additional Resources
    ❱
    1. Extra Utilities
    2. Scripts For Rhapsody
    3. Pipeline install bundle (docker-free)
  7. References
  8. Contact and Copyright
  9. Release Notes

BD Rhapsody™ Sequence Analysis Pipeline 4.0

Seven Bridges Setup


Steps

  1. Create a Seven Bridges account
  2. Create a new project
  3. Upload FASTQ files
  4. Upload reference files
  5. Import the pipeline app
  6. Create task and run the pipeline
  7. Download the output files