Footprinting issue

[leecon30]

Hi I've been trying to run footprint on my v5 Seurat object and i encounter this issue "Error in loadFUN(x, seqname, ranges) :
trying to load regions beyond the boundaries of non-circular sequence "chr1""

I have read previous threads where this problem was encountered with people for the addMotifs function. Interestingly i have no problem running addMotifs and this only appears when i use the footprinting function. I excluded the peaks found on contigs early on so i dont think that is the issue either.

Can you advise?

Cheers,
Lee

[timoast]

My guess is that there are some TF motif instances that are <250 bp from the end of a chromosome. Since the footprinting function extends +/-250 bp around each motif instance, it could extend beyond the end of a chromosome.

Which genome are you using? I haven't encountered this issue before since usually the ends of the chromosome are the telomeric repeats.

As a workaround you could try setting in.peaks=TRUE so that only motif instances inside peaks are considered. I will try to add a step that would remove TF motif instances close to the chromosome ends in a future Signac release