Change location of 'fragments' in multiome Seurat file
Entering edit mode
21 months ago
V ▴ 360


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:

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 • 1.4k views
Entering edit mode
15 months ago
V ▴ 360

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
  2. Add to your object
Fragments(HF1clean@assays$ATAC) <- NULL

 fragments <- CreateFragmentObject(path = "FullMultiome/atac_fragments.tsv.gz", cells = colnames(HF1), validate.fragments = TRUE)

Fragments(HF1clean@assays$ATAC) <- fragments

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