NAME

       Drop-seq_alignment.sh - perform Drop-seq tagging, trimming and alignment

DESCRIPTION

       USAGE: Drop-seq_alignment.sh [options] <unmapped-queryname-sorted.bam>

   OPTIONS
       -g <genomedir> Directory of STAR genome directory.  Required.

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

       -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: a new subdirectory in .

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

       -e     Echo commands instead of executing them.

       -k     Keep intermediate files

SEE ALSO

       create_Drop-seq_reference_metadata.sh(1)