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