Loom

LOOM format

ASAP accepts as input HDF5 files following the LOOM format, developped by Linnarson lab. Note that ASAP complies with 3.0.0 specifications.
10x

10x H5 format

ASAP accepts as input HDF5 files (.h5) from CellRanger developped by 10x Genomics [specifications].
TXT

Plain-text format (compressed or not)

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

Archive (compressed or not)

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.
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 in a file with extension .mtx. If several mtx files are present, a file named matrix.mtx is required and only this one will be used