Provided by: drop-seq-tools_2.5.4+dfsg-1_all bug

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)

create_Drop-seq_reference_metadata.sh             February 2021         CREATE_DROP-SEQ_REFERENCE_METADATA.SH(1)