create_from_cellranger (function)

Read a 10x Genomics cellranger folder and produce a corresponding Loom file.

loompy.create_from_cellranger(indir: str, outdir: str = None, genome: str = None) → str[source]

Create a .loom file from 10X Genomics cellranger output

Parameters:
  • indir (str) – path to the cellranger output folder (the one that contains ‘outs’)
  • outdir (str) – output folder wher the new loom file should be saved (default to indir)
  • genome (str) – genome build to load (e.g. ‘mm10’; if None, determine species from outs folder)
Returns:

Full path to the created loom file.

Return type:

path (str)

Remarks:
The resulting file will be named {sampleID}.loom, where the sampleID is the one given by cellranger.