Created
October 24, 2020 20:21
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RNA-seq read count normalization (TPM and RPKM)
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| #Rscript normalize_featurecounts.R counts_table.txt tpm ; | |
| #Rscript normalize_featurecounts.R counts_table.txt rpkm ; | |
| #Sample table### | |
| #GeneID<TAB>sample1<TAB>sample2<TAB>sample3<TAB>Length | |
| #Gene1<TAB>10<TAB>4<TAB>5<TAB>1500 | |
| #Gene2<TAB>20<TAB>43<TAB>60<TAB>4300 | |
| args<-commandArgs(TRUE) | |
| ccols <- c(2:30) # sample1_column:sampleN_column | |
| lcol <- 31 # Column containing length of sum of exons per gene (Please place it in last column to avoid confusion) | |
| expr <- read.table(args[1], header=T, sep="\t") | |
| rpkm <- function(counts, lengths) { | |
| rate <- counts / lengths | |
| rate / sum(counts) * 1e6 | |
| } | |
| tpm <- function(counts, lengths) { | |
| rate <- counts / lengths | |
| rate / sum(rate) * 1e6 | |
| } | |
| if(args[2]=="tpm"){ | |
| tpms <- apply(expr[,ccols], 2, function(x) tpm(x, expr[,lcol])) | |
| res <- cbind(as.character(expr[,1]),tpms) | |
| colnames(res)[1] <- colnames(expr)[1] | |
| write.table(res,paste0(args[1],".tpm"), sep="\t", row.names=F, quote=F) | |
| } | |
| if(args[2]=="rpkm"){ | |
| rpkms <- apply(expr[,ccols], 2, function(x) rpkm(x, expr[,lcol])) | |
| res <- cbind(as.character(expr[,1]),rpkms) | |
| colnames(res)[1] <- colnames(expr)[1] | |
| write.table(res,paste0(args[1],".rpkm"), sep="\t", row.names=F, quote=F) | |
| } |
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