Hi all,
I am currently learning scRNA-Seq analysis using Seurat, for which I downloaded the barcodes and features (and not the raw fastq files), and I am using the scripts that have been provided. In the set of files uploaded, the authors have not provided us with the *.h5 files to identify the doublets.
I was able to find a python script to generate the *.h5ad files from the barcodes and features, but when I run scanpy.read_10x_h5(), I get an error saying my file has more than one genome, and upon running it using any of the genome options (such as X, obs, varm), I get an error saying more files are needed.
My question now is, is it acceptable to generate the *.h5ad files from the barcodes and features, or is it to be done with the raw data? And if anyone is able to give me a solution to my above issue, it would be highly appreciated.
Thanks in advance
You need the counts as well, which are often in market matrix format. If you have all three of those files you can read them into scanpy directly with
read_10x_mtx.Hi,
Thnks for your reply. I do have the matrix file too. I will try that and update