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Map STAR Specifications

Process Details

  • Name: Map STAR
  • Process UUID: 20bdcd5e-ed05-11e8-9ce4-85221b21564c
  • Process Group: Alignment

Overview

This process implements the Spliced Transcripts Alignment to a Reference (STAR) software for high-speed RNA-seq read alignment. STAR uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure, outperforming other aligners by a factor of >50 in mapping speed. It can align 550 million 2 × 76 bp paired-end reads per hour to the human genome on a modest 12-core server. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is capable of mapping full-length RNA sequences.

This process is implemented in Bash, which invokes STAR aligner and samtools for read alignment and BAM file processing.

Key Functionality

  • High-speed RNA-seq alignment: Performs ultra-fast alignment of RNA-seq reads to reference genomes using STAR's optimized algorithms
  • Splice junction detection: Identifies canonical and non-canonical splice junctions, including chimeric (fusion) transcripts
  • Multiple output formats: Generates aligned BAM files, transcriptome alignments, and comprehensive alignment statistics
  • Quality assessment: Produces flagstat reports for alignment quality evaluation

Input/Output Specification

Inputs

Required Inputs

  • mate

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

  • reads

    • Description: Raw sequencing reads in FASTQ format for alignment
    • Format: fastq

  • starIndex

    • Description: Pre-built STAR genome index for the reference genome
    • Format: starIndex

Outputs

  • mapped_reads

    • Description: Primary aligned reads in BAM format
    • Format: bam

  • transcriptome_bam

    • Description: Reads aligned to transcriptome coordinates in BAM format
    • Format: bam

  • outputFileOut

    • Description: STAR output files containing alignment information
    • Format: out

  • outputFileTxt

    • Description: Text output files including alignment statistics
    • Format: txt

  • outputFileTab

    • Description: Tabular output files with alignment metrics
    • Format: tab

  • logOut

    • Description: STAR log files documenting the alignment process
    • Format: out

  • progressOut

    • Description: Progress tracking files from the alignment process
    • Format: out

Parameters & Settings

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

  • STAR Input Parameters

    • Description: Specify STAR input parameters
    • Default value: --runThreadN 10

  • Export Sense/Antisense BAM Files

    • Description: Export sense/antisense bam files
    • Available options: no (default), yes

References & Resources

  • Tool Documentation: Contact the team for details on STAR alignment parameters
  • Related Papers: Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., ... & Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21.