library(ChIPseeker) library(TxDb.Hsapiens.UCSC.hg38.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene library(clusterProfiler) library(org.Hs.eg.db) peaks <- readPeakFile("MACS_folder/pol2_chip/Pol_2pausing/pol2_diff_peak.bed") print(peaks) #peakAnno <- annotatePeak("merge/blast.bed", tssRegion=c(-3000, 3000), # TxDb=txdb, annoDb="org.Hs.eg.db") peakAnno <- annotatePeak(peaks, tssRegion=c(-1000, 1000), TxDb=txdb, annoDb="org.Hs.eg.db")
So this is basically what im doing to annotate the peaks.
Now the issue comes with annotation for example I see TLR4 annotated to this
118082896 118083202 307 * shp1_R1_peak_679 Exon (ENST00000413759.1/ENST00000413759.1, exon 1 of 1) 9 117708197 117708979 783 1 7099 ENST00000490685.1 374699 ENSG00000136869 TLR4
Now The peak is 679 as you can see from the IGV plot as well as annotated file. But when i see in IGV browser TLR4 is far away from the peak where i get the annotation.
So now is it an issue with the code im using or due to the inherent nature of the data.
Any help or suggestion would be really appreciated.