qsub/bash scripts for creating genome reference files (FASTA, STAR, etc.)

These scripts are intended for use with a cluster running Grid Engine and Environment Modules. They may also be run as standalone bash scripts using bash instead of qsub.

make_ucsc_references.qsub

Usage:

  qsub [qsub flags] make_ucsc_references.qsub
       [options] -b|--build [UCSC genome build]

Options:

  -b, --build          UCSC genome build (e.g., hg38, mm10, etc.)
  -o, --output-path    Path where output will be written (will be created if it does not exist)
                       (Default: ./[UCSC genome build]/)

Note: this script calls a wrapper script named picard that calls Java with the picard.jar file and 2GB maximum heap size.

make_ncbi_assembly_references.qsub

Usage:

  qsub [qsub flags] make_ncbi_assembly_references.qsub [options]
       -a|--assembly [assembly name]
       -n|--ncbi [NCBI accession]

Options:

  -a, --assembly       genome assembly name (e.g., 'A_J_v1', 'MesAur1.0')
  -n, --ncbi           NCBI accession (e.g., 'GCA_001624215.1', 'GCF_000349665.1')
  -o, --output-path    Path where output will be written (will be created if it does not exist)
                       (Default: ./[assembly name]/)

Note: this script calls a wrapper script named picard that calls Java with the picard.jar file and 2GB maximum heap size.

generate_star_genomes.qsub

Usage:

  qsub [qsub flags] generate_star_genomes.qsub [options]
       -r|--reference [reference name]
       -f|--fasta-path [Path to FASTA files]

Options:

  -r, --reference       Reference name
                        (e.g., hg38, mm10, bosTau9, MesAur1.0, etc.)
  -f, --fasta-path      Path to FASTA input files
                        (i.e., path containing 'base' folder, etc.)
  -o, --output-path     Path where output will be written (will be created if it does not exist)
                        (Default: ./[STAR version]/[reference name]/)
  -s, --star-version    Version of STAR to use
                        (if omitted, default STAR version is used)