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10x Genomics
Chromium Single Cell ATAC

HDF5 Feature-Barcode Matrix Format

In addition to MEX format, Cell Ranger ATAC also provides matrices in the Hierarchical Data Format (abbreviated HDF5 or H5). H5 is a binary format that can compress and access data much more efficiently than text formats such as MEX - which is especially useful when dealing with large datasets.

For more information on the format, see the Introduction to HDF5.

H5 files are supported in Python and we recommend the user to load h5 files in Python using one of the two ways described further below.

File format

The top-level of the file contains the matrix HDF5 group, with datasets describing the matrix listed under it.The file hierarchy would look something like this:

├── barcodes
├── data
├── features
│    ├── _all_tag_keys
│    ├── derivation
│    ├── feature_type
│    ├── genome
│    ├── id
│    └── name
├── indices
├── indptr
└── shape

Within each genome group, the matrix is 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, such that each barcode is represented by a contiguous chunk of data values.

barcodesstringBarcode sequences and their corresponding gem groups (e.g. AAACGGGCAGCTCGAC-1)
datauint32Nonzero UMI counts in column-major order
features/_all_tag_keysstringFeature attributes other than id, name, feature_type. For 2.1.0, this is simply genome, derivation.
features/derivationstringMechanism by which the feature was derived from primary feature types
features/feature_typestringPeaks or Motifs
features/genomestringGenome associated with each feature (e.g. hg19)
features/idstringPeak or motif name built into the reference (e.g. chr1:1000-2000, SPI1_HUMAN.MA0080.4)
features/namestringPeak or common motif name (e.g. chr1:1000-2000, SPI1_HUMAN.MA0080.4)
indicesuint32Row index of corresponding element in data
indptruint32Index into data / indices of the start of each column
shapeuint64Tuple of (n_rows, n_columns)

Loading matrices into Python

There are two ways to load the H5 matrix into Python:

1. Using cellranger-atac

This method requires that you add cellranger-atac/lib/cellranger/lib/python to your $PYTHONPATH.

E.g. if you installed Cell Ranger ATAC into /opt/cellranger-atac-2.1.0, then you would call:

$ export PYTHONPATH=/opt/cellranger-atac-2.1.0/cellranger-atac-cs/2.1.0/lib/cellranger/lib/python:$PYTHONPATH

Then in Python, call:

import cellranger.matrix as cr_matrix
filtered_matrix_h5 = "/opt/sample345/outs/filtered_peak_bc_matrix.h5"
peak_matrix = cr_matrix.CountMatrix.load_h5_file(filtered_matrix_h5)
matrix = peak_matrix.m

2. Using PyTables

This method is more involved, and requires the SciPy and PyTables libraries.

import collections
import scipy.sparse as sp_sparse
import tables
FeatureBCMatrix = collections.namedtuple('FeatureBCMatrix', ['ids', 'names', 'barcodes', 'matrix'])
def get_matrix_from_h5(filename, genome):
    with tables.open_file(filename, 'r') as f:
            group = f.get_node(f.root, 'matrix')
        except tables.NoSuchNodeError:
            print "Matrix group does not exist in this file."
            return None
        feature_group = getattr(group, 'features').read()
        ids = getattr(feature_group, 'id').read()
        names = getattr(feature_group, 'name').read()
        barcodes = getattr(group, 'barcodes').read()
        data = getattr(group, 'data').read()
        indices = getattr(group, 'indices').read()
        indptr = getattr(group, 'indptr').read()
        shape = getattr(group, 'shape').read()
        matrix = sp_sparse.csc_matrix((data, indices, indptr), shape=shape)
        return FeatureBCMatrix(ids, names, barcodes, matrix)
filtered_matrix_h5 = "/opt/sample345/outs/filtered_tf_bc_matrix.h5"
tf_bc_matrix = get_matrix_from_h5(filtered_matrix_h5)
matrix = tf_bc_matrix.m