error in initiate_grn()

[GouQiao]

Dear developer,

I want to use a multiome object processed by signac and seurat in Pando. But I met error for the first step.

Obj<-initiate_grn(

• Obj,
• regions = NULL,
• peak_assay = "ATAC",
• rna_assay = "RNA",
• exclude_exons = TRUE
• )

Error in compatibleSeqnames(rep(seqnames(x), elementNROWS(y)), seqnames(y@unlistData)) : Level set of 'x' must be subset of that of 'y', or vice versa In addition: Warning messages: 1: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:

• in 'x': GL456210.1, GL456216.1, GL456233.1, JH584292.1, JH584304.1
• in 'y': chrMT Make sure to always combine/compare objects based on the same reference genome (use suppressWarnings() to suppress this warning). 2: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:
• in 'x': GL456210.1, GL456216.1, GL456233.1, JH584292.1, JH584304.1
• in 'y': chrMT Make sure to always combine/compare objects based on the same reference genome (use suppressWarnings() to suppress this warning).

Could you tell me how to fix this?

[GouQiao]

solved by the codes following: DefaultAssay(Obj) <- 'ATAC' granges(Obj) main.chroms <- standardChromosomes(BSgenome.Mmusculus.UCSC.mm10) keep.peaks <- as.logical(seqnames(granges(Obj)) %in% main.chroms) Obj <- Obj[keep.peaks, ]

[joschif]

This is probably related to the gene annotations and the peaks having different sequences or chromosomes, which causes errors for I/GRanges. As you suggested, matching the sequence levels should fix it