convert matrix files from 10X (single cell) to h5 file
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7 months ago
Sara ▴ 260

For my single cell data, I have matrix files from 10X including (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for all my samples. I am trying to convert them to one h5 file per sample. to do so I used Create_10X_H5 function from a R package called scCustomize using the following command:

Create_10X_H5(raw_data_file_path = "/home/Matrixes_raw/sample_filtered_feature_bc_matrix/", save_file_path = "/home/Matrixes_raw/sample_filtered_feature_bc_matrix/", save_name = "sample1.h5").

but I keep getting error with the following log message:

10X data contains more than one type and is being returned as a list containing matrices of each type.
Import complete. Start write to H5
Error in if (length(gene.id) != length(gene.symbol) || length(gene.id) !=  : 
  missing value where TRUE/FALSE needed

Do you know how to fix it or do you know any other way to create h5 files?

scRNA-seq • 741 views
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Your data is multimodal data therefore Create_10X_H5 did not work. I m not sure if scCustomize provides any function to convert your multimodal data into h5 file. However, you can check in this link.

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