Space Ranger1.3, printed on 10/05/2024
In addition to the MEX format, 10x Genomics also provides matrices in the Hierarchical Data Format (HDF5 or H5). H5 is a binary format that compresses and accesses data more efficiently than text formats such as MEX, which is useful when dealing with large datasets. H5 files are supported in both Python and R.
For more information on the format, see the Introduction to HDF5.
Note: Space Ranger generates an output file with per-molecule information in HDF5 format. General information about the HDF5 file format described here applies to the molecule_info.h5
file. Refer to the Molecule Info (H5) documentation for more specific details.
filtered_feature_bc_matrix.h5 └── matrix [HDF5 group] ├── barcodes ├── data ├── features [HDF5 group] │ ├── _all_tag_keys │ ├── feature_type │ ├── genome │ ├── id │ ├── name │ └── target_sets [For Targeted GEX, HDF5 group] │ └── [target set name]] ├── indices ├── indptr └── shape
The hierarchy is same for raw_feature_bc_matrix.h5
file.
The contents of the .h5
file can be examined using HDFView
software or the h5dump
command.
.h5
h5dump -n filtered_feature_bc_matrix.h5ls
HDF5 "filtered_feature_bc_matrix.h5" {
FILE_CONTENTS {
group /
group /matrix
dataset /matrix/barcodes
dataset /matrix/data
group /matrix/features
dataset /matrix/features/_all_tag_keys
dataset /matrix/features/feature_type
dataset /matrix/features/genome
dataset /matrix/features/id
dataset /matrix/features/name
group /matrix/features/target_sets
dataset /matrix/features/target_sets/[target set name]
dataset /matrix/indices
dataset /matrix/indptr
dataset /matrix/shape
}
}
.h5
(e.g. the /matrix/barcodes
dataset)h5dump -d matrix/barcodes filtered_feature_bc_matrix.h5 | head -n 15 HDF5 "filtered_feature_bc_matrix.h5" { DATASET "matrix/barcodes" { DATATYPE H5T_STRING { STRSIZE 18; STRPAD H5T_STR_NULLPAD; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; } DATASPACE SIMPLE { ( 3468 ) / ( 3468 ) } DATA { (0): "AAACAAGTATCTCCCA-1", "AAACAATCTACTAGCA-1", "AAACACCAATAACTGC-1", (3): "AAACAGAGCGACTCCT-1", "AAACAGTGTTCCTGGG-1", "AAACATTTCCCGGATT-1", (6): "AAACCGGGTAGGTACC-1", "AAACCGTTCGTCCAGG-1", "AAACCTAAGCAGCCGG-1", (9): "AAACCTCATGAAGTTG-1", "AAACGAAGAACATACC-1", "AAACGAGACGGTTGAT-1", (12): "AAACGCCCGAGATCGG-1", "AAACGGGCGTACGGGT-1", "AAACGGTTGCGAACTG-1",
The top level of the file contains a single HDF5 group, called matrix
, and metadata stored as HDF5 attributes. Within the matrix
group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and spot-barcodes associated with the matrix rows and columns, respectively.
Column | Type | Description |
---|---|---|
barcodes | string | Barcode sequences and their corresponding library identifiers (for example, AAACGGGCAGCTCGAC-1 ). The library identifier is always -1 for spaceranger count runs of individual capture areas, and a small integer that identifies distinct capture areas in the output of spaceranger aggr |
data | uint32 | Nonzero UMI counts in column-major order |
indices | uint32 | Zero-based row index of corresponding element in data |
indptr | uint32 | Zero-based index into data / indices of the start of each column, that is the data corresponding to each barcode sequence |
shape | uint64 | Tuple of (# rows, # columns) indicating the matrix dimensions |
The matrix entries are stored in Compressed Sparse Column (CSC) format. For more details on the format, see this SciPy introduction. CSC represents the matrix in column-major order, so that each barcode is represented by a contiguous chunk of data values.
The feature reference is stored as an HDF5 group called features
, within the matrix
group. Note that for Targeted Gene Expression samples, the features
dataset in the filtered matrix H5 file will not contain non-targeted genes, and the feature indices in target_sets
are updated accordingly.
There are multiple packages that allow import of HDF5 file into R as shown in the example code below (edit path to the H5 file in red).
# set path to the h5 file h5_path = "/opt/sample345/outs/filtered_feature_bc_matrix.h5" # Method 1 # load the Bioconductor rhdf5 package library(rhdf5) # read in the file and examine its contents filtered_hs <- H5Fopen(h5_path) h5ls(filtered_hs) # Method 2 # load package library(Seurat) # read in the file and examine its contents filtered_hs <- Read10X_h5(h5_path) head(filtered_hs, 10)
There are two ways to load the H5 matrix into Python:
This method requires adding spaceranger/lib/python to your $PYTHONPATH. For example, if you installed Space Ranger into /opt/spaceranger-1.3.1, then you can call the following script to set your PYTHONPATH:
$ source spaceranger-1.3.1/sourceme.bash
Then in Python, the matrix can be loaded using the cellranger.matrix module as follows (edit the path to the H5 file in red):
import cellranger.matrix as cr_matrix filtered_h5 = "/opt/sample345/outs/filtered_feature_bc_matrix.h5" filtered_matrix_h5 = cr_matrix.CountMatrix.load_h5_file(filtered_hs)
This method is more involved, and requires the SciPy and PyTables libraries. Edit the path to the H5 file in red.
import collections import scipy.sparse as sp_sparse import tables CountMatrix = collections.namedtuple('CountMatrix', ['feature_ref', 'barcodes', 'matrix']) def get_matrix_from_h5(filename): with tables.open_file(filename, 'r') as f: mat_group = f.get_node(f.root, 'matrix') barcodes = f.get_node(mat_group, 'barcodes').read() data = getattr(mat_group, 'data').read() indices = getattr(mat_group, 'indices').read() indptr = getattr(mat_group, 'indptr').read() shape = getattr(mat_group, 'shape').read() matrix = sp_sparse.csc_matrix((data, indices, indptr), shape=shape) feature_ref = {} feature_group = f.get_node(mat_group, 'features') feature_ids = getattr(feature_group, 'id').read() feature_names = getattr(feature_group, 'name').read() feature_types = getattr(feature_group, 'feature_type').read() feature_ref['id'] = feature_ids feature_ref['name'] = feature_names feature_ref['feature_type'] = feature_types tag_keys = getattr(feature_group, '_all_tag_keys').read() for key in tag_keys: feature_ref[key] = getattr(feature_group, key).read() return CountMatrix(feature_ref, barcodes, matrix) filtered_h5 = "/opt/sample345/outs/filtered_feature_bc_matrix.h5" filtered_matrix_h5 = get_matrix_from_h5(filtered_hs)