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Mimseq Specifications

Process Details

  • Name: mimseq
  • Process UUID: 4GOHtn5Igmp3ek052J3TkIf7fUyqrb
  • Process Group: Transcript Quant.

Overview

This process executes tRNA analysis on a set of FASTQ input reads using the Mimseq tool. Mimseq is designed for comprehensive analysis of tRNA sequencing data, providing clustering, mapping, and quantification capabilities for both genomic and mitochondrial tRNAs.

This process is implemented in Bash.

Key Functionality

  • tRNA Sequence Analysis: Performs comprehensive analysis of tRNA reads from FASTQ files using genomic and mitochondrial tRNA references
  • Clustering and Mapping: Clusters similar tRNA sequences and maps reads with configurable mismatch tolerance and coverage thresholds
  • Multi-mapping Handling: Controls handling of reads that map to multiple tRNA loci with adjustable parameters
  • Report Generation: Produces PDF and PNG visualization files for analysis results

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: FASTQ sequencing files containing tRNA reads
    • Format: FASTQ

  • Groups

    • Description: Text file defining sample groups and experimental design
    • Format: TXT

  • Genomic tRNAs

    • Description: Reference sequences for genomic tRNAs
    • Format: FASTA

  • tRNA Output Reference

    • Description: Additional tRNA reference sequences for output processing
    • Format: FASTA

  • Mitochondrial tRNAs

    • Description: Reference sequences for mitochondrial tRNAs
    • Format: FASTA

  • Mate

    • Description: Mate pair information for paired-end sequencing data
    • Format: mate

  • Control

    • Description: Control condition specification for differential analysis
    • Format: control

Outputs

  • Output Directory

    • Description: Complete analysis results directory containing all Mimseq output files
    • Format: Directory

  • PDF Report

    • Description: Comprehensive PDF report with analysis results and visualizations
    • Format: PDF

  • PNG Images

    • Description: Individual visualization files in PNG format
    • Format: PNG

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Experiment Name

    • Description: Name of experiment. Note, output files and indices will have this as a prefix
    • Default value: experiment

  • Mimseq Parameters

    • Description: Mimseq parameters
    • Default value: --cluster --cluster-id 0.95 --threads 10 --min-cov 2000 --max-mismatches 0.1 --max-multi 1 --remap --remap-mismatches 0.075

References & Resources

  • Tool Documentation: Contact the team for details on mimseq