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star_batch

A star batch script

Batches up files in a directory and runs the STAR aligner on them.

STAR: ultrafast universal RNA-seq aligner
Alexander Dobin1,*, Carrie A. Davis1, Felix Schlesinger1, Jorg Drenkow1, Chris Zaleski1, Sonali Jha1, Philippe Batut1, Mark Chaisson2 and Thomas R. Gingeras1

Usage:
star_batch.py -i inputDirectory -e fileExtension -g genomeDir -o outputDirectory [-t threads -r --clip5pNbases clip5pNbases --outFilterMultimapNmax outFilterMultimapNmax]

Arguments:

Required:

  • -i INPUT_DIR, --input INPUT_DIR
    • The input directory to analyze
  • -o OUTPUT_DIR, --output OUTPUTDIR
    • The output directory
  • -g INDEX_DIR, --genomeDir INDEX_DIR
  • genomeDir string: path to the directory where genome files are stored
  • -e EXTENSION_STRING, --ext EXTENSION_STRING
    • The file extension to match. File extensions must start with '.' to be valid!

Optional:

  • -h, --help
    • show this help message and exit
  • -r
    • Recursive input directory
  • -t threads, --threads PROCESSORS
    • The number of processors to use. DEFAULT = 90% of CPUs int(cpu_count() * .90)
  • --base CLIP5PBASE
    • clip5pNbases: int: number(s) of bases to clip from 5p of each mate. If one value is given, it will be assumed the same for both mates. DEFAULT = 6
  • --outFilterMultimapNmax REPEAT
    • outFilterMultimapNmax: int: read alignments will be output only if the read maps fewer than this value, otherwise no alignments will be output. DEFAULT = 10

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