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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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Multiome object on new machine, CoveragePlot Error: TabixFile: Fragment file is not indexed #1730

Closed NathanKochhar closed 1 week ago

NathanKochhar commented 1 week ago

An error that I came across and found a work around for is “Error: TabixFile: Fragment file is not indexed.”, which arose from calling CoveragePlot when using a seurat multiome object that was created on one machine and loaded in on another. The solution is to also move the fragment files to the new machine and change the fragments path within the ATAC assay of the seurat object.

obj@assays[["ATAC"]]@fragments[[1]]@path <- "new/frag/path"

I hope this helps anyone that came across this issue!

timoast commented 1 week ago

I recommend to use the UpdatePath() function which will verify that the fragment file is the same as was originally used when constructing the object, see example here: https://stuartlab.org/signac/articles/data_structures#changing-the-fragment-file-path-in-an-existing-fragment-object