Hi, I want to use chipseeker package to annotate my ATAC-Seq peaks. but I get the error as below:
>library(GenomicFeatures) >library(ChIPseeker) > require(GenomicFeatures) >txdb <- makeTxDbFromGFF("data/Aqu3.1_Gene.checked.gff3") >peak1 <- readPeakFile("data/macs/1hps_1_peaks.narrowPeak") >promoter <- getPromoters(TxDb = txdb, upstream = 3000, downstream = 3000) > tagMatrix <- getTagMatrix(peak1, windows = promoter) **>Error in getTagMatrix(peak1, windows = promoter) : width of windows should be equal...**
then I checked the promoter and found that:
> promoter GRanges object with 0 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> ------- seqinfo: 2349 sequences from an unspecified genome; no seqlengths
could anyone know what is wrong with this? Thanks very much!!!