ucscXena/xenaH5

python scripts for converting 10x genomics single cell RNAseq data to Xena dense matrix file

xenaH5

Python scripts for converting 10x genomics single cell RNAseq data to Xena dense matrix file, particular for handling the large HDF5 Gene-Barcode Matrix Format.

---

What is 10x genomics HDF5 Gene-Barcode Matrix Format

https://support.10xgenomics.com/single-cell/software/pipelines/latest/advanced/h5_matrices

xenaH5 Requirement

python 2

python modules
    h5py
    numpy
    uuid

xenaH5 Usage

1. Get a basic information about the h5 file, find out group name
python h5_info.py your_h5file

2. Slow and simple convertion
python h5_xena.py Gene-Barcode_Matrix_h5 groupname output_tsv_file

3. Fast convertion
    3.1 python h5_transpose.py Gene-Barcode_Matrix_h5 groupname output_transposed_h5
    3.2 python h5_xena_fast.py output_transposed_h5 groupname output_tsv_file

Load xena dense matrix file (tsv) into your xena hub

http://xena.ucsc.edu/private-hubs/