Skip to content

Mimseq Groups Specifications

Process Details

  • Name: mimseq_groups
  • Process UUID: 2SoFekdqaxmfSvHMNmV11AxYKabhhX
  • Process Group: Misc.

Overview

This process specifies sample groups for future Mimseq analysis by creating a groups file that maps sample names to their corresponding experimental conditions. It organizes samples into control and treatment groups, enabling downstream comparative analysis workflows in the Mimseq pipeline for tRNA sequencing data.

This process is implemented in Bash, which invokes a Perl script for group file generation.

Key Functionality

  • Sample Group Organization: Maps individual sample files to their experimental group labels (control vs treatment groups)
  • Group File Generation: Creates a structured text file containing sample-to-group assignments for downstream analysis
  • Multi-Treatment Support: Handles multiple treatment groups with distinct names and sample compositions
  • Control Group Definition: Establishes the reference/control group for comparative analyses

Input/Output Specification

Inputs

This process does not require file inputs - it generates group assignments based on user-specified parameters.

Outputs

  • groups

    • Description: Tab-delimited text file mapping sample filenames to their experimental group labels
    • Format: txt

  • control

    • Description: Control group identifier for downstream processing
    • Format: control

Parameters & Settings

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

  • Control/Wild-type group name

    • Description: Control/Wild-type group name
    • Default value: ""

  • Control Group Samples

    • Description: Comma-separated list of sample names (please don't include the extension of the file e.g. for control.rep1.fq -> use control.rep1)
    • Default value: ""

  • Treatment group name for figures

    • Description: Treatment group name for figures
    • Default value: ""

  • Treatment Group Samples

    • Description: Comma-separated list of samples (please don't include the extension of the file) (e.g. for first group: treat1.rep1, treat1.rep2 and for second group click add button and enter: treat2.rep1, treat2.rep2)
    • Default value: ""

References & Resources

  • Tool Documentation: Contact the team for details on the Perl script implementation