Re-analyzing scRNA seq data from GSE129788 #9031
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Chanistics
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I am new on the scRNA seq analysis.
I want to re-analyze the public single cell RNA seq dataset with our research focus.
but, GSE129788 provides gene expression data and combined metadata, which is not common form (barcodes, matrix, genes).
to further analysis, I tried to make Seurat object with gene expression data and combined metadata.
first, I split the combined metadata manually, and then make Seurat object based on the this website. (https://divingintogeneticsandgenomics.com/post/reuse-the-single-cell-data-how-to-create-a-seurat-object-from-geo-datasets/).
however, incorrect form of Seurat object was produced. I cannot extract cluster markers. (printed as 'feature4689')
when I use GSE129788 or this kind of public dataset, how can I make the correct form of seuratobject?
is there any pipelines for GEO dataset to Seurat?
Thank you for your response in advance.
best regards,
chan.
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