# STAR：构建小鼠的基因组索引

## 来源

https://www.gencodegenes.org/mouse/

https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/

http://asia.ensembl.org/info/about/species.html

## 步骤

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    zcat XL789vs123/XL1/default_s.fq.gz  head #这个例子只有50, 因此 sjdbOverhang 为49

    wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M29/GRCm39.primary_assembly.genome.fa.gz
    wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M29/gencode.vM29.primary_assembly.annotation.gtf.gz

    gunzip *.gz

    conda activate star
    nano 2.sh
    chmod +x 2.sh

    #!/bin/sh
    STAR \
    --runMode genomeGenerate \
    --genomeDir index \
    --genomeFastaFiles GRCm39.primary_assembly.genome.fa \
    --sjdbOverhang 49 \
    --sjdbGTFfile gencode.vM29.primary_assembly.annotation.gtf \
    --runThreadN 8

- human和mouse推荐从gencode上下载
- 其他物种可以从NCBI上下载，也可以从ENSEMBL上下载，需要参考基因组fasta文件和对应的gtf注释

组织测序
STAR：构建小鼠的基因组索引
https://occdn.limour.top/1932.html
Author
Limour
Posted on
July 2, 2022
Licensed under
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