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LuyiTian / FLAMES

Full-length transcriptome splicing and mutation analysis
GNU General Public License v3.0
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Using transcript_count.csv.gz matrix with popular analysis tools #21

Open rakszewska opened 2 years ago

rakszewska commented 2 years ago

I'm struggling to convert transcript_count.csv.gz matrix to a Seurat or AnnData object? Any help and advice would be appreciated.

LuyiTian commented 2 years ago

Hi, The file format is basically the same as a gene counting matrix from scRNAseq data, the only difference is that the first two colunms contain both gene id and then transcript id. if you want to do transcript level analysis you could only use the transcript id in the matrix, otherwise you can ignore the transcript id column, merge the rows from the same gene id to do a gene-level analysis.