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create_from_cellranger() incompatible w/ Cellranger 3.0

See original GitHub issue

Having installed CellRanger 3.0 (v3.0.1), I tried to generate loom files using create_from_cellranger() (loompy v2.0.16). I got the following:

File "/home/user/virtualenv-15.2.0/pyEnv2/lib/python3.6/site-packages/loompy/", line 1025, in create_from_cellranger
    genome = [f for f in os.listdir(matrix_folder) if not f.startswith(".")][0]
FileNotFoundError: [Errno 2] No such file or directory: '/data/user/chromium/samples/10X_069/outs/filtered_gene_bc_matrices'

According to the release notes of CellRanger 3.0, there are some changes in the output file format (quoting some points bellow):

Output File Format Changes

  • The file formats of the gene-barcode matrix (now called the feature-barcode matrix) have changed to accomodate Feature Barcoding results.
  • The mtx and barcodes.tsv files are now gzipped to save disk space
  • The genes.tsv file has been renamed features.tsv.gz, and contains extra columns indicating the feature_type of each gene / feature.

Issue Analytics

  • State:closed
  • Created 5 years ago
  • Comments:6 (3 by maintainers)

github_iconTop GitHub Comments

slinnarssoncommented, Jan 31, 2019

I pushed 2.0.17 just now and it should be in pypi shortly.

Note: conda loompy is not updated, so please use pip install -U loompy to update

pl-kicommented, Dec 14, 2018

Right, I forgot to push this, will do shortly!

Read more comments on GitHub >

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