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