Hi, I am trying to upload an h5ad file to MapMyCells after integrating them, and my rows are cell barcodes and columns and gene names in mice, but MapMyCells still give me an input file error, any suggestions and help are greatly appreciated
My run ID is Run ID: 1722459927475-091483ac-4405-4708-80c0-f255a23e7ae5, and I’m using jupyter notebook for integration
Hi,
You should have been able to download an error log file (validation_log.txt) with the specific error message in it. I can see the same message. It is very long, but it starts with
Cell IDs need to be unique.
The following cell IDs were repeated in your obs dataframe:
'AAACCAATCTAATGGA-1' occurred 2 times
'AAACCAGGTATGGTAG-1' occurred 2 times
'AAAGGCTTCACATTCG-1' occurred 2 times
'AAATCACCATTCCTTT-1' occurred 2 times
...
So it looks like many (possibly all) of the cell IDs in your h5ad file are duplicated. MapMyCells won’t know how to handle that, as it won’t know how to associate mapping results with input cells.
Thank you so much! It helps a lot!!!