BD Rhapsody™ Sequence Analysis Pipeline
Setup and Running Guide
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Input Files and Parameters
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FASTQ files
Reference Files
Pipeline Parameters
Seven Bridges Setup
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Seven Bridges Account
Create a New Project
Upload FASTQ Files
Upload Reference Files
Import the Pipeline App
Create Task and Run the Pipeline
Download the Output
Local Server Setup
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System and Software Installation
Input Specification File
Run the Pipeline with CWL-runner
Pipeline Steps and Algorithms
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Read Quality Filter
Annotate R1 Cell Label and UMI
Align and Annotate R2 Reads
Valid Read Pairs
Molecules and Error Correction
Determine Putative Cells
Sample Tag Analysis
Generate Expression Matrix Datatables
Annotate BAM
TCR and BCR Analysis
ATAC-Seq Analysis
Output Files
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Metrics Summary CSV
Pipeline Report HTML
Cell-by-Feature Data Tables
BAM and BAM Index
Single-cell Analysis Tool Inputs
Bioproduct Statistics
Sample Tag Metrics
Sample Tag Calls
Sample Tag Folders
VDJ Metrics
VDJ Per Cell
VDJ Contigs AIRR
Protein Aggregates Experimental
Immune Cell Classification
Dimensionality Reduction
ATAC Fragments
ATAC Transposase Sites
ATAC Peaks
ATAC Peak Annotation
ATAC Data Tables
ATAC Metrics
Troubleshooting Guide
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Access Log Files
Output Metrics and Associated Problems
Skim Sequencing for Assessing Library Quality
Additional Resources
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Extra Utilities
Scripts For Rhapsody
Pipeline install bundle (docker-free)
References
Contact and Copyright
Release Notes
Light
Rust
Coal
Navy
Ayu
BD Rhapsody™ Sequence Analysis Pipeline 2.3
Local Server Setup
Steps
System and software installation
Create the input specification file
Run the pipeline using CWL-runner