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• Obtain the filtered Count matrix files (h5 or HDF5) files and Spatial outputs (Figure 1) for each sample. Please note that the 10x Genomics Space Ranger output can be count matrix data as 1 filtered .h5 file per sample or sparse matrix files for each sample as 3 files (two .csv with one .mtx or two .tsv with one .mtx for each sample). The spatial output files should be in compressed format (.zip). The high resolution image can be uploaded and is optional. 

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You can wait a few minutes for the download to complete, or check the download progress by selecting Queue then View queued tasks... to view the Queue (Figure 4).Navigate to the appropriate files for each sample (Figure 4). Please note that the 10x Genomics Space Ranger output can be count matrix data as 1 filtered .h5 file per sample or sparse matrix files for each sample as 3 files (two .csv with one .mtx or two .tsv with one .mtx for each sample). The spatial output files should be in compressed format (.zip). The high resolution image can be uploaded and is optional. 

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Once the download completes, the sample table will appear in the Data tab, with one row per sample (Figure 5).

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