Drop-seq_alignment.sh - perform Drop-seq tagging, trimming and alignment
USAGE: Drop-seq_alignment.sh [options] <unmapped-queryname-sorted.bam>
-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
create_Drop-seq_reference_metadata.sh(1)