Several input variables are required to make the metadata file. These are detailed below:
- Assay type: The type of assay used (e.g., CITE, DOGMA, etc.)
- Experiment ID: A unique identifier for the experiment
- Historical number: A unique identifier, likely for the pool of cells loaded onto the 10x chip. For example, if you have two pools and load the first onto two GEMs and the second onto one, the first experiment would have a historical number of 1 and replicate names of A and B, and the second pool would have a historical number of 2 and a replicate name of A.
- Replicate: The replicate number for the experiment: see above.
- Modality: The modality of the experiment (e.g., Gene expression, ATAC, ADT, etc.)
- Chemistry: The chemistry used for the experiment (e.g., 3' v2, 3' v3, etc.). For more information see here.
- Index type: The type of index used (Single index or dual index). Refer to the assay used, and the plate or primers used to index your library.
- Index: The index used for the experiment. This is the barcode used to identify the sample.
- Species: The species of the sample (Human or mouse)
- Number of donors: The number of donors in this GEM well, used for donor deconvolution. Human only, write NA for mouse.
- ADT file name: The name of the ADT file used for the experiment. Exclude .csv suffix. This is the name of the file that contains ADT barcodes. The format must match the format for your experiment, detailed here.
Please make one metadata file per sequencing run.
