002单细胞分析2025-单细胞10x ATAC-seq自定义物种参考基因组的构建（斑马鱼）

1.激活环境和软件

conda info -e
conda activate cellranger36

cd cellranger-atac-2.1.0/
pwd
/home/be/besinglecell/soft/cellranger-atac-2.1.0
export PATH=/home/be/besinglecell/soft/cellranger-atac-2.1.0:$PATH
source sourceme.bash

2.下载GTF和Fastq文件

wget http://ftp.ensembl.org/pub/release-113/gtf/danio_rerio/Danio_rerio.GRCz11.113.gtf.gz
 
gunzip Danio_rerio.GRCz11.113.gtf.gz
 
 
wget http://ftp.ensembl.org/pub/release-113/fasta/danio_rerio/dna/Danio_reri o.GRCz11.dna.primary_assembly.fa.gz
 
gunzip Danio_rerio.GRCz11.dna.primary_assembly.fa.gz

3.建立一个config文件写入参考基因的相关信息 保存为config.json

{
  organism: "Danio"
  genome: ["GRCz11"]
  input_fasta: ["/home/be/besinglecell/danio/Danio_rerio.GRCz11.dna.primary_assembly.fa"]
  input_gtf: ["/home/be/besinglecell/danio/Danio_rerio.GRCz11.113.filtered.gtf"]
}

4.构建参考基因组

准备好 config.json 后，运行如下命令来生成参考包：

cellranger-atac mkref --config=config.json 

最终生成一个参考基因GRCz11文件夹 参考包

参考

Creating a Reference Package with cellranger-atac mkref - 10x Genomics

Creating a Reference Package with cellranger-atac mkref - 10x GenomicsCell Ranger ATAC and Loupe Browser are software applications for analyzing and visualizing Epi ATAC (formerly Single Cell ATAC) data produced by the 10x Genomics Chromium platform.https://www.10xgenomics.com/support/software/cell-ranger-atac/latest/analysis/inputs/creating-a-reference-package-mkrefDocumentation - 10x Genomicshttps://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/software-analysis

Cell Ranger - 10x GenomicsA set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.https://www.10xgenomics.com/support/software/cell-ranger/latest

Tutorials - 10x GenomicsA set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials

Cell Ranger ATAC10XCell Ranger ATAC 是一组处理Single Cell ATAC 数据的分析管道。下载安装https://mp.weixin.qq.com/s/w4hydEPuTPIe9ISgXcFvSA?poc_token=HN46D2ij_USX3Qcv6xS03XQn-XnbtDDe3i12ljO3

cellranger 操作笔记-2：构建绵羊单细胞转录组参考基因组_cellranger参考基因-CSDN博客文章浏览阅读4.8k次，点赞5次，收藏9次。本文详细介绍了如何为单细胞测序数据准备参考基因组，包括从Ensembl下载绵羊的参考基因组和注释文件，使用cellranger工具过滤非编码转录本，创建10X兼容的参考基因组，并解决线粒体基因缺失的问题。此外，还展示了如何添加外源基因如GFP到参考基因组中，以供后续分析使用。https://blog.csdn.net/flashan_shensanceng/article/details/115718337?utm_source=miniapp_weixin

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