Question: ChIPseeker TSS plot
0
gravatar for CalM
2.9 years ago by
CalM0
Toulouse
CalM0 wrote:

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 • 1.1k views
ADD COMMENTlink modified 2.8 years ago by Guangchuang Yu1.1k • written 2.9 years ago by CalM0
Answer: ChIPseeker TSS plot
0
gravatar for Guangchuang Yu
2.8 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

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.

ADD COMMENTlink written 2.8 years ago by Guangchuang Yu1.1k
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