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sameStrand=TRUE in annotatePeak not working properly #257

@helloworldABCD1234

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@helloworldABCD1234

My bed file is full of positive chains, but the Promoter TSS, exon, and UTR annotated have negative chains. What do you think? I used sameString=TRUE, and the coordinates in the bed should have been annotated to the positive chain gene. Now there are a lot of annotations to the negative chain, just because the positive chain coordinates are relatively close to the negative chain coordinates, such as chr1 1-200 +, it should be annotated to Intergenc, because chr1 1-200 - exon, the negative chain is an exon, and chr1 1-200 coincide with the negative chain coordinates, so I annotated to the negative chain's exon. What should I do to annotate the positive chain coordinates to the positive chain and obtain the correct annotation? Help me plz

The positive chain of the bed should be annotated to the Promoter TSS, Exon, UTR of the positive chain gene, rather than the negative chain

library(ChIPseeker)
peak <- readPeakFile("1.bed")
library(TxDb.Drerio.UCSC.danRer11.refGene)
txdb <- TxDb.Drerio.UCSC.danRer11.refGene
promoter <- getPromoters(TxDb = txdb, upstream = 3000, downstream = 3000)
tagMatrix <- getTagMatrix(peak, windows = promoter)

peakAnno <- annotatePeak(
peak,
tssRegion = c(-3000, 3000),
TxDb = txdb,
annoDb = "org.Dr.eg.db",
sameStrand = TRUE
)
plotAnnoPie(peakAnno)

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