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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!!!
Best Hf