Entering edit mode
12 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?
Your data is multimodal data therefore
Create_10X_H5
did not work. I m not sure ifscCustomize
provides any function to convert your multimodal data into h5 file. However, you can check in this link.