Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
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Palmira • 0
@214f06b5
Last seen 5 weeks ago
Spain

I am trying to annotate a set of peaks (mapped to the mouse reference genome mm39) using ChIPseeker and TxDb.Mmusculus.UCSC.mm39.refGene as txdb object (see below). Most peaks are well annotated but I have some peaks that are not correctly annotated. For example: All of these peaks: chr1:80000590-80000639, chr10:79744980-79745309, chr12:13495785-1349590, and many more are annotated to gene: 19862 (Rnu6), but this gene is in fact located to chr17. Here the code I used:

library(ChIPseeker)
library(TxDb.Mmusculus.UCSC.mm39.refGene)
txdb <- TxDb.Mmusculus.UCSC.mm39.refGene
peaks<-readPeakFile(peakfile = "03_Peak_Lists/ChIP_peaks.bed")
peakAnno<-annotatePeak(peaks, tssRegion=c(-1000,100), TxDb=txdb)
peakAnnot<-as.data.frame(peakAnno@anno)

Could anyone tell me what is the problem? I have also tried adding

library(org.Mm.eg.db)
peaks<-readPeakFile(peakfile = "03_Peak_Lists/ChIP_peaks.bed")
peakAnno<-annotatePeak(peaks, tssRegion=c(-1000,100), TxDb=txdb, annoDb="org.Mm.eg.db")

But I have the same problem. Could anyone help me? Thank you!

TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate • 70 views
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