LinkPeak() reveal no significant peaks

[sylestiel]

Hi Tim,

Is it essential to call peaks using MACS2 when integrating multiple multiome datasets? If so at which point do I incorporate that step?

My output for LinkPeaks is as follows:

DefaultAssay(integrated) <- "ATAC"

integrated <- RegionStats(integrated, genome= Mmulatta)
Warning in RegionStats.default(object = regions, genome = genome, verbose = verbose, :
Not all seqlevels present in supplied genome

link peaks to genes

link peaks to genes

integrated <- LinkPeaks(

• object = integrated,
• peak.assay = "ATAC",
• expression.assay = "SCT",
• genes.use = c("LEF1")
• )
  Testing 1 genes and 156706 peaks
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s

No significant links found

My seqlevelsStyle()
seqlevelsStyle(integrated) <- ### "NCBI"

Is there any possibility of a vignette which outlines the major steps of Multiome integration in the near future? That would be really helpful.

Looking forward to your feedback.

Thanks!