关于分析猪的单细胞数据进行质控时没有匹配到线粒体基因这件事

匹配参考基因组的“MT”

grep '^MT\s' Sus_scrofa.Sscrofa11.1.112.filtered.gtf > PIG.MT.genes.txt

整理得到线粒体基因的ID和symbol名

ENSSSCG00000018065		ND1
ENSSSCG00000018069		ND2
ENSSSCG00000018075		COX1
ENSSSCG00000018078		COX2
ENSSSCG00000018080		ATP8
ENSSSCG00000018081		ATP6
ENSSSCG00000018082		COX3
ENSSSCG00000018084		ND3
ENSSSCG00000018086		ND4L
ENSSSCG00000018087		ND4
ENSSSCG00000018091		ND5
ENSSSCG00000018092		ND6
ENSSSCG00000018094		CYTB

在R中，运行

library(dplyr)
library(Seurat)
library(patchwork)
library(ggplot2)

setwd("F:/PY/IMF_snRNA_seq/out/data")
#批量读取4个10X单细胞转录组数据文件夹：
folders=list.files('./',pattern='[12]$')
folders

sceList = lapply(folders,function(folder){ 
  CreateSeuratObject(counts = Read10X(folder), 
                     project = folder )
})
#运行merge函数,合并四个样本
IMF.big.merge <- merge(sceList[[1]], 
                 y = c(sceList[[2]],sceList[[3]],sceList[[4]]), 
                 add.cell.ids = folders, 
                 project = "LDM_merge")
IMF.big.merge

mt.genes=c('ND1','ND2',
     'COX1','COX2','ATP8',
     'ATP6','COX3','ND3',
     'ND4L','ND4',
     'ND5','ND6','CYTB')
#查看是否存在以上基因
gene_presence <- mt.genes %in% rownames(IMF.big.merge)
print(gene_presence)
#[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#[13] TRUE
IMF.big.merge[["percent.mt"]] <- PercentageFeatureSet(IMF.big.merge, pattern = "ND1|ND2|COX1|COX2|ATP8|ATP6|COX3|ND3|ND4L|ND4|ND5|ND6|CYTB")

参考资料：
猪的单细胞分析如何过滤线粒体基因