scDAPA:从单细胞转录组数据中检测可变聚腺苷酸化(APA) - 简书

10X_RNA/Development/scDAPA/extractGenes.sh -i10X_RNA/pipeline2.1/database/10X_Ref/refdata-cellranger-GRCh38-1.2.0/genes/genes.gtf -o hg38.gene.gff export PATH=bedtools2/bin/:$PATH10X_RNA/Development/scDAPA/annotate3Ends.sh -d 10X_RNA/Development/scDAPA/example/result/ -g 10X_RNA/Development/scDAPA/example/hg38.gene.gff # 1. only compare two specific cell groups scDAPAdetect(file1=\'./result/1.anno\',file2=\'./result/2.anno\',type=\'f2f\',output_dir=\'./stat\') # 2. compare every two cell groups stored in the ./result directory scDAPAdetect(dir=\'./result\',type=\'d\',output_dir=\'./stat\',bin_size=100,count_cutoff=20) dp = scDAPAview(files=c(\'./result/1.anno\',\'./result/2.anno\'),alt_names=c(\'cell_A\',\'cell_B\'),gtf=gtf,gene_id=\'ENSG00000160062\',legend.position = c(0.2,0.8)) # customize colour theme library(ggsci) dp + scale_colour_aaas() # customize legend title dp + labs(colour = \"Cell type\") # customize legend position dp + theme(legend.position = c(0.6, 0.9)) # customize simultaneuouly dp + scale_colour_aaas() + labs(colour = \"Cell type\") + theme(legend.position = c(0.6, 0.9))