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bedapub / besca

BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis
https://bedapub.github.io/besca/
GNU General Public License v3.0
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new 10x mtx version #342

Open wangjiawen2013 opened 3 months ago

wangjiawen2013 commented 3 months ago

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 ?

kohleman commented 3 months ago

Hi @wangjiawen2013, thanks for your request. We will look into this as soon as we have the capacity to do so. Thanks, Manuel