Seurat 2.2
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16 months ago
twillafup • 0

I have output created from the Optimus pipleine on Terra and am trying to duplicate a workflow that was develkoped with Seurat 2.2. I currently have Seurat version 4.x installed.

How can I "downgrade" my existing Seurat or at least install v2 in parallel?

Pipeline: https://app.terra.bio/#workspaces/featured-workspaces-hca/HCA_Optimus_Pipeline.

Right now, I'm trying to create a Seurat object using Read10X: The folder has 3 needed files and am getting:

Error in Read10X("~/Fieldwork/fieldwork_data/output/", gene.column = 2,  : 
  Barcode file missing. Expecting barcodes.tsv.gz

Would installing Seurat 2.2 fix the error? Or is there a way in Seurat 4 to make it work?

Thanks

anvil 2.2 terra seurat barcode.gz • 623 views
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In bash: ls ~/Fieldwork/fieldwork_data/output/ ?

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(base) pvillafuerte@supermicro:~/Fieldwork/fieldwork_data/output$ ls barcodes barcodes.tsv features.tsv matrix.mtx

The error I'm getting is :

Read10X( "~/Fieldwork/fieldwork_data/output/", gene.column = 2, cell.column = 1, unique.features = TRUE, strip.suffix = FALSE )

Error in Read10X("~/Fieldwork/fieldwork_data/output/", gene.column = 2, : Barcode file missing. Expecting barcodes.tsv.gz

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There is your error. Files are probably expected to be gzipped, it clearly says .tsv.gz

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