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