Here we will provide some real-world examples for different purposes when you run TSSr.

We will use data from this paper as an example.

The data has been submitted to the NCBI BioProject database under accession number PRJNA510689.

1. Generate .bw / .bedGraph format files from CAGE (CAGE-like) data

If you want to generate both plus and minus strand TSS singal in .bw format or bedGraph.

##########Load packages################
library(TSSr)
library(Rsamtools)
library(BSgenome.Spombe.NCBI.ASM294v231)
##########Change below lines################
genomeName <- "BSgenome.Spombe.NCBI.ASM294v231"
species <- ""
mergeIndex <- c(1,1)
organismName <- "Schizosaccharomyces pombe"
inputFiles <- c(
"SRR8360238_Aligned.sortedByCoord.out.bam",
"SRR8360239_Aligned.sortedByCoord.out.bam"
)
inputFilesType <- "bam"
sampleLabels <- c(
                  "SRR8360238"
                 ,"SRR8360239"
                 )
output_file <- "pombe.star.RData"
###########################
myTSSr <- new("TSSr", genomeName = genomeName
            ,inputFiles = inputFiles
            ,inputFilesType = inputFilesType
            ,sampleLabels = sampleLabels
            ,sampleLabelsMerged = organismName
            ,mergeIndex = mergeIndex
            ,organismName = organismName)
getTSS(myTSSr)
exportTSStable(myTSSr, data = "raw", merged = "FALSE")
plotCorrelation(myTSSr, samples = "all")

exportTSStoBedgraph(myTSSr, data = "raw", format = "bedGraph") 
exportTSStoBedgraph(myTSSr, data = "raw", format = "BigWig")


save(TSSr, file = output_file)

2. Generate a correlation map between biological replicates.

3. TBA