I'm interested in using ChIPseeker to plot profiles of ChIP peaks binding to TSS regions on drosophila data.
The problem is when I'm modifying the TSS region (from -1kb to 2kb): the plot is showing 2 peaks at 0 (TSS position) and 1000 pb, instead of one unique peak corresponding to the TSS position that I obtain when I use the default TSS region (-3kb, 3kb).
It seems to me that the gene orientation is not taken into account, resulting in a gap between the TSS positions of the different windows.
Here is my script:
library(TxDb.Dmelanogaster.UCSC.dm6.ensGene) txdb <- TxDb.Dmelanogaster.UCSC.dm6.ensGene file <- "./peaks.bed" peak <- readPeakFile(file[]) promoter <- getPromoters(TxDb=txdb, upstream=1000, downstream=2000) tagMatrix <- getTagMatrix(peak, windows=promoter) plotAvgProf(tagMatrix, xlim=c(-1000, 2000), xlab="Genomic Region (5'->3')", ylab = "Read Count Frequency")
What am I missing ?
Thanks a lot