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Check Build STAR Index Specifications

Process Details

  • Name: Check_Build_STAR_Index
  • Process UUID: 17fc7842-e169-11e9-be30-e0aab38271b1
  • Process Group: Index

Overview

This process builds a STAR index using specified genome FASTA files and a gene annotation GTF file, and stores it in a designated location for subsequent genomic alignment. The process intelligently checks if a STAR index already exists and either builds a new one or creates a symbolic link to an existing index. It includes configuration, index generation, storage, and symbolic linking steps to optimize computational resources.

This process is implemented in Bash, which invokes the STAR aligner for genome index generation.

Key Functionality

  • Index Validation: Checks for the existence of a valid STAR index by looking for the SA file
  • Conditional Index Building: Builds a new STAR index only if one doesn't already exist
  • Symbolic Linking: Creates symbolic links to existing indexes to avoid redundant computation
  • Multi-threaded Processing: Utilizes multiple threads for efficient index generation

Input/Output Specification

Inputs

Required Inputs

  • genome

    • Description: Reference genome sequence file containing the complete genomic DNA sequences
    • Format: FASTA

  • gtfFile

    • Description: Gene annotation file containing transcript and exon coordinates for splice junction detection
    • Format: GTF

Outputs

  • starIndex
    • Description: Complete STAR genome index directory containing all necessary files for RNA-seq alignment
    • Format: starIndex

Parameters & Settings

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

  • star build parameters
    • Description: star build parameters
    • Default value: --runThreadN 5

References & Resources

  • Tool Documentation: STAR Manual
  • Related Papers: Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T.R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21.