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Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. STAR has a potential for accurately aligning long (several kilobases) reads that are emerging from the third-generation sequencing technologies.
  • STAR genomeGenerate

    genomeGenerate option directs STAR to run genome indices generation job.

  • STAR alignReads

    In this step user supplies the genome files generated in the 1st step, as well as the RNA-seq reads (sequences) in the form of FASTA or FASTQ files. STAR maps the reads to the genome, and writes several output files, such as alignments (SAM/BAM), mapping summary statistics, splice junctions, unmapped reads, signal (wiggle) tracks etc.

  • STAR inputAlignmentsFromBAM

    Processing of BAM file without re-alignment.

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