Question

ChIPseeker TSS plot

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CalM • 0

@calm-12235

Last seen 4.5 years ago

Toulouse

Hi,

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[[1]])

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

chipseeker plotAvgProf • 2.0k views

ADD COMMENT • link updated 7.8 years ago by Guangchuang Yu ★ 1.2k • written 7.9 years ago by CalM • 0

score 0 · Answer 1 · 2017-02-13

ChIPseeker do take consideration of gene orientation.


library(ChIPseeker)

library(TxDb.Hsapiens.UCSC.hg19.knownGene)

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

files <- getSampleFiles()

peak <- readPeakFile(files[[4]])  

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")

I tested with the above code and couldn’t see any gap.