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.
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 ?
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
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