Change location of 'fragments' in multiome Seurat file
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Entering edit mode
7 months ago
V ▴ 320

Hello,

I have a multiome dataset of RNA +ATAC seq that was given to me as an analysed .RData file by a collaborator. This is already integrated and fully analysed.

When I attempt to visualise something in the multiome Seurat object using something like the below :

CoveragePlot(test, region = 'CD8A', features = 'CD8A', assay = 'ATAC', expression.assay = 'SCT', peaks = FALSE)


I get an error saying :

Error: TabixFile: file(s) do not exist:
'/Users/m/Data/Multiome_1220/atac_fragments.tsv.gz'
'/Users/m/Data/Multiome_1220/atac_fragments.tsv.gz.tbi'


I am not 'm' so it would seem that Rstudio is looking for these files in the original directory on my collaborators machine rather on mine in the pwc. Does anyone know how I can edit the stored path to the fragments.tsv.gz file and replace it with my own? I've tried the 'SetFragments' argument that use to be active in Signac but it is no longer working. Any help would be much appreciated. Thank you

RNA-Seq R Seurat Signac ATAC-Seq • 346 views
3
Entering edit mode
7 weeks ago
V ▴ 320

To add an answer to this because I figured it out in the end :

1. Reset the current fragments object in the Seurat
1. Make a new path
Fragments(HF1clean@assays$ATAC) <- NULL fragments <- CreateFragmentObject(path = "FullMultiome/atac_fragments.tsv.gz", cells = colnames(HF1), validate.fragments = TRUE) Fragments(HF1clean@assays$ATAC) <- fragments