Using dropEst output for Seurat

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4.2 years ago

annadv • 0

Hello All,

I have obtained some scRNAseq data from a repository and the data are in count.matrices.rds files, which appear to be created using dropEst with "-V" option, so each file contains "exon", "intron" and "spanning" (exon/intron spanning) lists of counts.

I was wondering if anyone could advise me on how to turn these lists into a Seurat object? I am used to have "counts", so I'm not sure how to obtain such data from these 3 lists - do I merge them and then use as.Seurat function to turn the result into a Seurat object? If so, how should I merge them?

Thank you very much for your help and advice!

Regards, Anna

Seurat dropEST rds files • 1.0k views

ADD COMMENT • link 4.2 years ago by annadv • 0

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Unless you are doing RNA velocity or have another compelling reason, you general use just the exon counts for scRNA-seq. If the data is formatted with features as row names, and cell barcodes as column names, then you can use the Seurat function CreateSeuratObject to start the analysis.

ADD REPLY • link 4.2 years ago by rpolicastro 13k

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Thank you very much for your answer! Should I also use the spanning list, since it is "exon/intron spanning", or should I use just the "exon" list?