create_from_fastq (function)

Use kallisto to build a loom file from a set of fastq files.

loompy.create_from_fastq(out_file: str, sample_id: str, fastqs: List[str], index_path: str, samples_metadata_file: str, n_threads: int = 1, temp_folder: str = None, synchronous: bool = False) → None[source]
Parameters

  • String like "10xv2" or None to read the technology from the sample metadata file (technology) –

  • Expected number of cells captured in the sample, or None to read the number from the sample metadata file (expected_n_cells) –

  • Path to tab-delimited file with one header row OR path to sqlite database with one table called "sample" (samples_metadata_file) –

Remarks:
Samples metadata table should contain these columns:

name Sample name (i.e. sample id) chemistry 10x chemistry version (v1, v2 or v3) targetnumcells Number of cells expected in the sample