---
name: "create_Drop-seq_reference_metadata.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/create_Drop-seq_reference_metadata.sh"
---

# create\_Drop-seq\_reference\_metadata.sh(1)

create Drop-seq reference metadata bundle

## NAME

create\_Drop-seq\_reference\_metadata.sh - create Drop-seq reference metadata bundle

## DESCRIPTION

USAGE: create\_Drop-seq\_reference\_metadata.sh \[options\]

### OPTIONS

**-n** \<name\> Name for reference metadata set to be created.  Required.

- **-r** \<referencefasta\>

  Reference fasta of the Drop-seq reference metadata bundle.  Required.

- **-s** \<species\>

  Species.  Required.

- **-g** \<gtf\>

  Gene annotation file.  Required.

- **-f** \<filtered-gene-biotype\>

  Annotations with the given gene\_biotype will be filtered. Multiple values may be specified by using this argument more than once, and/or by providing a comma-separated list. Use ValidateReference command to see the gene\_biotypes in your GTF in order to decide what to exclude.  Default: not gene biotypes are filtered.

**-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: Value of 132153TMPDIR environment variable.

- **-a** \<STAR\_path\>

  Full path of STAR.  Default: STAR is found via PATH environment variable.

- **-b** \<bgzip\_path\>

  Full path of bgzip: Default: bgzip is found via PATH environment variable.

- **-i** \<samtools\_path\>

  Full path of samtools.  Default: samtools is found via PATH environment variable.

- **-v**

  verbose

- **-e**

  merely echo commands instead of executing

## SEE ALSO

[**Drop-seq\_alignment.sh**(1)](/Drop-seq_alignment.sh/1.md)