File Formats

Supported input formats for ASAP.

Loom

LOOM format

ASAP accepts as input HDF5 files following the LOOM format, developed by the Linnarsson lab. Note that ASAP complies with the 3.0.0 specifications.

10x

10x H5 format

ASAP accepts as input HDF5 files (.h5) from CellRanger developed by 10x Genomics. See the official specifications.

Text

Plain-text format (compressed or not)

ASAP accepts as input simple plain-text matrices, with column delimiters such as tabulation, comma, semi-colon, or space. First or last column as gene names is optional; gene names are mapped to the Ensembl database. First line as cell/sample names is optional too. The file can be compressed.

H5AD

H5AD format

From release 8, ASAP supports AnnData files (.h5ad). These files contain matrices, observations, variables, and embeddings in a single portable container that can be produced by tools such as Scanpy.

TAR

Archive

ASAP supports archive files that contain several datasets in a plain-text format. You can select which dataset to take as input in the interface.

TGZ

Archive compressed

ASAP supports compressed archive files that contain several datasets in a plain-text format. You can select which dataset to take as input in the interface.

ZIP

Compressed

ASAP supports compressed files (zip and gzip, and from release 8, we added bzip2 and xz).

MEX

MEX/MTX

ASAP requires all three files to be archived/compressed in a single file (.tar, .tar.gz, .gz, .zip, .bz2, .tar.bz2). The files need to be named:

  • barcodes.tsv
  • genes.tsv or features.tsv
  • The main data matrix with extension .mtx. If several .mtx files are present, a file named matrix.mtx is required and only this one will be used.
RDS

RDS

From release 8, ASAP supports Seurat objects (.rds).