小鼠参考基因组id转换gtf文件chb 自己注释 从官网下载相应的基因中注释文件gse155802 getmatrix genecode

 参考基因组在很多网站都可以下载到

Index of /pub/release-93/gtf/mus_musculus (ensembl.org)http://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/ 我想要研究的基因组

我怎么知道是这个的呢 ，因为这篇文献里面提到

References - 3.0.0 (November 19, 2018)

nohup wget -c ftp://ftp.ensembl.org/pub/release-93/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz &
 
 
gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
 
 
 
 
nohup wget -c ftp://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens/Homo_sapiens.GRCh38.93.gtf.gz &
 
gunzip Homo_sapiens.GRCh38.93.gtf.gz

Download Cell Ranger - Official 10x Genomics SupportA 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/downloads

• Human reference, GRCh38 (Ensembl 93)https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#grch38_3.0.0
• Human reference, hg19 (Ensembl 87)https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#hg19_3.0.0
• Mouse reference, mm10 (Ensembl 93)

所以我就在cellranger官网上找到了这个Build Notes for Reference Packages -Software -Single Cell Gene Expression -Official 10x Genomics Support

点进去之后，出现代码

Mouse reference, mm10 (includes mouse V(D)J genes)
wget ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
 
 
wget ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz
gunzip Mus_musculus.GRCm38.93.gtf.gz

根据代码下载的地址  就可以找到自己要复现的基因组地址了！这里我只需要gtf格式就行啦

Index of /pub/release-93/gtf/mus_musculus (ensembl.org)

手动下载之后

如何处理gtf文件呢？在R语言中读取GTF文件的最好方法 · 大专栏 (dazhuanlan.com)

链接里给了好多方法  哈哈哈

我就用第一个吧 ，开始！

####参考基因组id转换gtf文件 https://www.dazhuanlan.com/insafe/topics/975998
#BiocManager::install("rtracklayer")
library(rtracklayer)
 
#https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build
#把Mus_musculus.GRCm38.93.gtf.gz下载下来 为什么下载这个呢？http://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/
gtf_df=rtracklayer::import('Mus_musculus.GRCm38.93.gtf.gz')
getwd()

更改seurat行名 seurat基因名

如何给Seurat对象的基因重命名？【基因名转换】2022-07-27 - 简书 (jianshu.com)

#创建函数 改名字
RenameGenesSeurat <- function(obj , 
                              newnames ) { 
  # Replace gene names in different slots of a Seurat object. Run this before integration. Run this before integration. 
  # It only changes obj@assays$RNA@counts, @data and @scale.data.
  print("Run this before integration. It only changes obj@assays$RNA@counts, @data and @scale.data.")
  RNA <- obj@assays$RNA
  
  if (nrow(RNA) == length(newnames)) {
    if (length(RNA@counts)) RNA@counts@Dimnames[[1]]            <- newnames
    if (length(RNA@