Seurat 2.2
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
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twillafup •
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Failed to link 10x file in Rstudio
written by KOUSTAV •
In bash:
ls ~/Fieldwork/fieldwork_data/output/?(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
There is your error. Files are probably expected to be gzipped, it clearly says .tsv.gz