Drop-seq_alignment.sh(1)

perform Drop-seq tagging, trimming and alignment

Section 1 drop-seq-tools bookworm source

Description

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