new 10x mtx version
- Dominant language
- Python
- Stars
- 50
- Forks
- 17
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 3
Description
Hi,
bc.export.X_to_mtx() output the previous mtx generated by cellranger 2:
barcodes.tsv genes.tsv matrix.mtx
The latest cellranger generated distinct outputs now:
barcodes.tsv.gz features.tsv.gz matrix.mtx.gz
"genes.tsv" in cellranger2 has become "features.tsv.gz" in cellranger3. There are two columns in genes.tsv but three columns in features.tsv.gz. Could you update bc.export.X_to_mtx() to support the latest mtx ?
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Research direction
Start by locating bc.export.X_to_mtx() and inspect how it handles the Cell Ranger 2 files barcodes.tsv, genes.tsv, and matrix.mtx. Verify support for the Cell Ranger 3 files barcodes.tsv.gz, features.tsv.gz with three columns, and matrix.mtx.gz; done means the latest mtx output is accepted.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100