Using transcript_count.csv.gz matrix with popular analysis tools

[rakszewska]

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

[LuyiTian]

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.