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Prepare Input Velocyto Specifications

Process Details

  • Name: prepare_input_velocyto
  • Process UUID: ce532f5bd9d64bbd8266fdab27a44015
  • Process Group: Misc.

Overview

This process prepares input files for RNA velocity analysis using Velocyto by standardizing file naming conventions and organizing BAM files with their corresponding barcode information. The process handles different input scenarios, including direct BAM file inputs or Cell Ranger output directories, and creates a consistent file structure required for downstream velocity analysis.

This process is implemented in Bash.

Key Functionality

  • File Standardization: Renames input BAM files and associated index files to standardized names (input.bam, input.bam.bai)
  • Barcode Processing: Handles barcode files from either direct input or Cell Ranger filtered feature-barcode matrix
  • Directory Organization: Creates organized output directory structure for velocity analysis workflow
  • Flexible Input Handling: Processes both individual BAM files and Cell Ranger output directories

Input/Output Specification

Inputs

Optional Inputs

  • Output Directory

    • Description: Target directory for organized output files
    • Format: Directory

  • BAM File

    • Description: Aligned sequencing reads in BAM format with corresponding index file
    • Format: BAM

  • Input File TSV

    • Description: Tab-separated file containing barcode or metadata information
    • Format: TSV

Outputs

  • BAM File

    • Description: Standardized BAM file renamed as input.bam with corresponding index file
    • Format: BAM

  • Input File TSV

    • Description: Processed barcode file in compressed TSV format for velocity analysis
    • Format: TSV

References & Resources

  • Tool Documentation: This process serves as a preprocessing step for Velocyto analysis workflows