How to read tsv data as dgcmatrix
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4 months ago
Alex ▴ 20

Update: Solved. The barcodes provided in the metadata and count matrix are not the same.

One is “xyz-1”, another is “xyz.1”. Just need to correct the barcodes.

I will post some photos later as references for people who might encounter similar issues in the future . Thanks

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I have a tsv count matrix and a tsv metadata. I read both files by read_tsv("filename"), so they become tibble.

Next, I tried to CreateSeuratObject(counts = counts, meta.data=meta). It failed.

I wonder what is the standard way to convert the tsv matrix into dgcMatrix, and create a seurat object from them?

scRNA-seq seurat • 474 views
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Post the error message or more details on why it has failed.

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it failed is not an adequate description, please add details. Likely the format itself (dense or sparse matrix) is not the issue here since Seurat can accept dense (=normal) matrix.

Anyway, as(your_matrix, "CsparseMatrix").

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