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Cellranger Fastq Collect Specifications

Process Details

  • Name: cellranger_fastq_collect
  • Process UUID: ZT9ZLdovrJMrUCIku8JDIKdV6wBoWB
  • Process Group: SingleCell

Overview

This process prepares FASTQ files for Cell Ranger analysis by organizing them into a standardized directory structure. It collects and moves FASTQ files into a new reads directory, creating the proper file organization required for downstream single-cell RNA sequencing analysis workflows.

This process is implemented in Bash.

Key Functionality

  • File Organization: Creates a standardized reads directory structure for Cell Ranger compatibility
  • FASTQ Collection: Moves all input FASTQ files into the newly created reads_fastq directory
  • Directory Preparation: Establishes the BCL directory path structure required for Cell Ranger processing

Input/Output Specification

Inputs

Required Inputs

  • Reads
    • Description: FASTQ files containing single-cell RNA sequencing reads to be organized for Cell Ranger analysis
    • Format: FASTQ

Outputs

  • BCL Directory

    • Description: Directory path structure (/reads) created for Cell Ranger compatibility
    • Format: BCL directory

  • Reads

    • Description: Organized FASTQ files moved into the reads_fastq directory structure
    • Format: FASTQ

References & Resources

  • Tool Documentation: This process uses standard file system operations and does not require external tool documentation