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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Motif analysis with Signac species #409

Closed widsquid closed 3 years ago

widsquid commented 3 years ago

Hello, I have been getting a great deal of use out of your tools lately, thanks as always for the excellent work.

I am wondering if the species (9606) in the mouse brain vignette is actually human. I have run my data through with both 9606 and 10090 (mouse?) and get different results, albeit with slight overlap. Is there a reason to use human here or should it be mouse? Thanks so much. W

https://satijalab.org/signac/articles/motif_vignette.html

# Get a list of motif position frequency matrices from the JASPAR database pfm <- getMatrixSet( x = JASPAR2020, opts = list(species = 9606, all_versions = FALSE) )

# add motif information mouse_brain <- AddMotifs( object = mouse_brain, genome = BSgenome.Mmusculus.UCSC.mm10, pfm = pfm )

timoast commented 3 years ago

See #58

You can certainly use whichever motif set makes the most sense for your analysis

widsquid commented 3 years ago

Thanks, yes it definitely seemed that some pertinent motifs were absent from one species or the other. W ps thanks for pointing me to issue #58, sorry I did not find it first as I think it adequately answered my question.