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A. thaliana annotation mistakes #230

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BHB26 opened this issue Jan 19, 2024 · 0 comments
Open

A. thaliana annotation mistakes #230

BHB26 opened this issue Jan 19, 2024 · 0 comments

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@BHB26
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BHB26 commented Jan 19, 2024

Dear Pr Guangchuang Yu

I am using ChIPseeker to annotate peaks from macs2 peak calling. I am working on Arabidopsis thaliana and i am using
TxDb.Athaliana.BioMart.plantsmart51.

my code:

Open_region_MacsCalls_Anno <- annotatePeak(eval((text=paste0(path,"/atac_openRegions_peaks.narrowPeak"))),
TxDb = TxDb.Athaliana.BioMart.plantsmart51,tssRegion=c(-0,0))

problem example:
seqnames 1
start 49891
end 49966
width 76
annotation 3' UTR
geneChr 1
geneStart 47234
geneEnd 49304
geneStrand 2
geneId AT1G01090
distanceToTSS -587

image

We are on the minus strand and the annotation doesn't match with the region of the peak because the peak is before the TSS so it can't be 3' UTR.
Could you help me to understand this result please ?

Sincerely

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