bedapub / bedapub/besca

new 10x mtx version

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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

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