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Check Build Rsem Index Specifications

Process Details

  • Name: Check Build Rsem Index
  • Process UUID: 17fc7a18-e169-11e9-be30-e0aab38271b1
  • Process Group: Index

Overview

This process checks the conditions for building an RSEM index and handles the creation of the index based on the specified parameters. It supports different reference types (Bowtie, Bowtie2, STAR) and stores the index in a designated directory. The process intelligently checks if an existing index is available before creating a new one, optimizing computational resources.

This process is implemented in Bash, which invokes RSEM tools for reference preparation and indexing.

Key Functionality

  • Index Validation: Checks for existing RSEM index files to avoid redundant processing
  • Multi-Reference Support: Supports Bowtie, Bowtie2, and STAR reference types for alignment
  • Automated Index Creation: Builds RSEM reference index using genome FASTA and GTF annotation files
  • Flexible Input Handling: Supports both GTF-based and transcript-to-gene mapping approaches

Input/Output Specification

Inputs

Required Inputs

  • Genome

    • Description: Reference genome sequence in FASTA format
    • Format: FASTA

  • GTF File

    • Description: Gene annotation file containing transcript and gene information
    • Format: GTF

Optional Inputs

None specified.

Outputs

  • RSEM Index
    • Description: Complete RSEM reference index for RNA-seq quantification
    • Format: rsemIndex

Parameters & Settings

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

  • Transcript to Gene Map

    • Description: Activated when transcript_to_gene_map path is entered into this field. It will use transcript_to_gene_map file instead of gtf file (optional)
    • Default value: ""

  • RSEM Build Parameters

    • Description: Additional parameters for RSEM reference preparation
    • Default value: "-p 16"

References & Resources

  • Tool Documentation: Contact the team for details on RSEM reference preparation tools
  • Related Papers: Li, B., & Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics, 12(1), 323.