https://github.com/carlescn/scrnaseq-tools

This is a set of bash wrapper scripts for STAR that simplify it's setup and use with a set of pre-defined parameters.
https://github.com/carlescn/scrnaseq-tools

bash bioinformatics danio-rerio linux scrna-seq zebrafish

Last synced: 2 days ago
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This is a set of bash wrapper scripts for STAR that simplify it's setup and use with a set of pre-defined parameters.

• Host: GitHub
• URL: https://github.com/carlescn/scrnaseq-tools
• Owner: carlescn
• License: gpl-3.0
• Created: 2022-11-28T12:33:13.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2023-06-13T17:40:27.000Z (over 1 year ago)
• Last Synced: 2024-11-09T04:37:30.892Z (about 2 months ago)
• Topics: bash, bioinformatics, danio-rerio, linux, scrna-seq, zebrafish
• Language: Shell
• Homepage:
• Size: 91.8 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# scRNAseq-tools

[![GPLv3 license](https://img.shields.io/badge/License-GPLv3.0-blue.svg)](https://github.com/carlescn/scRNAseq-tools/blob/main/LICENSE)

[![made-with-bash-5.1](https://img.shields.io/badge/Made%20with-Bash%205.1-1f425f.svg?logo=gnubash)](https://www.gnu.org/software/bash/)

[![Linux](https://img.shields.io/badge/OS-Linux-yellow.svg?logo=linux)](https://www.linux.org/)

[![STAR-2.7.9a](https://img.shields.io/badge/STAR-2.7.10b-darkgreen.svg)](https://github.com/alexdobin/STAR)

## STARsolo scripts

This is a set of bash scripts I wrote

as a wrapper for [STARsolo](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md)

to simplify it's setup

and for running it with a set of parameters

which try to replicate the output of

[10x Genomics Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).

The scripts are located under the directory `./bin/starsolo`

([see documentation](/bin/starsolo/README.md)):

- **`starsolo-setup-linux-x86_64.sh`**:

  downloads the [STAR executable](https://github.com/alexdobin/STAR/)

  and the [whitelists from 10xGenomics](https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-whitelist-).

- **`starsolo-gen-idx-danio-rerio.sh`**:

downloads the reference genome GRCz11 for the sp. Danio_rerio

  from [ENSEMBL](https://www.ensembl.org/Danio_rerio/Info/Index)

  and generates the STAR genome index.

- **`run-starsolo.sh`**:

  runs the STARsolo algorithm with some preset parameters.

## SRA scripts

Because I needed some experiment data to test the STARsolo scripts,

I also wrote a couple of scripts

to obtain FASTQ files from the

[SRA repository](https://www.ncbi.nlm.nih.gov/sra/docs/).

These download the raw data files from the SRA repository

and extract the original FASTQ files

using the `fastq-dump` tool from

[SRA-toolkit](https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit).

The obtained FASTQ files should be equivalent to the output of

[cellranger count](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).

The scripts are located under the directory `./bin/sra`

([see documentation](/bin/sra/README.md)):

- **`get-fastq-dump.sh`:**

  downloads the tool fastq-dump from the

  [SRA-toolkit](https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit).

- **`sra-to-cellranger-count.sh`:**

  downloads the raw data from the SRA repositories

  for the given ID(s) and extracts the original FASTQ files.

## Workflow example

Finally,

I provide a workflow example

(`workflow_example.sh`)

that uses all these scripts to:

1. Download and setup all the tools.

1. Download some example data from the SRA repositories.

1. Run STARsolo to obtain a cell-feature count matrix.