Open rejo27 opened 5 months ago
Dear Pr Guangchuang Yu I am using the ChIPseeker package to annotate the peaks of ATACseq. The command is
txdb <- makeTxDbFromGFF("/Users/ltan/Documents/my.gff",format="gff") peaks <- "/Users/ltan/Downloads/ATAC.peak.bed" peakAnno <- annotatePeak(peaks, TxDb = txdb,tssRegion = c(-2000, 0), addFlankGeneInfo=T,flankDistance = 5000)
But I found that although there are multiple genes within 5000 bp upstream and downstream of some peaks, most of the flank_gene_distances columns are 0. such as
flank_gene_distances
I don't know why. Looking forward to your reply
Dear Pr Guangchuang Yu I am using the ChIPseeker package to annotate the peaks of ATACseq. The command is
But I found that although there are multiple genes within 5000 bp upstream and downstream of some peaks, most of the
flank_gene_distancescolumns are 0. such asI don't know why. Looking forward to your reply