---
name: "Drop-seq_alignment.sh"
section: "1"
platform: "linux"
package: "drop-seq-tools"
version: "3.0.2+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Drop-seq_alignment.sh"
---

# Drop-seq\_alignment.sh(1)

perform Drop-seq tagging, trimming and alignment

## 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

## SEE ALSO

[**create\_Drop-seq\_reference\_metadata.sh**(1)](/create_Drop-seq_reference_metadata.sh/1.md)