NAME

       create_Drop-seq_reference_metadata.sh - create Drop-seq reference metadata bundle

DESCRIPTION

       USAGE: create_Drop-seq_reference_metadata.sh [options]

   OPTIONS
       -n <name> Name for reference metadata set to be created.  Required.

       -r <referencefasta>
              Reference fasta of the Drop-seq reference metadata bundle.  Required.

       -s <species>
              Species.  Required.

       -g <gtf>
              Gene annotation file.  Required.

       -f <filtered-gene-biotype>
              Annotations  with  the  given gene_biotype will be filtered. Multiple values may be
              specified  by  using  this  argument  more  than  once,  and/or  by   providing   a
              comma-separated  list.   Use  ValidateReference command to see the gene_biotypes in
              your GTF in order to decide what  to  exclude.   Default:  not  gene  biotypes  are
              filtered.

       -d   <dropseq_root>   Directory   containing  Drop-seq  executables.   Default:  directory
       containing this script.

       -o <outputdir>
              Where to write output bam.  Default: current directory.

       -t <tmpdir>
              Where to  write  temporary  files.   Default:  Value  of  132153TMPDIR  environment
              variable.

       -a <STAR_path>
              Full path of STAR.  Default: STAR is found via PATH environment variable.

       -b <bgzip_path>
              Full path of bgzip: Default: bgzip is found via PATH environment variable.

       -i <samtools_path>
              Full path of samtools.  Default: samtools is found via PATH environment variable.

       -v     verbose

       -e     merely echo commands instead of executing

SEE ALSO

       Drop-seq_alignment.sh(1)