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Question: 10x to cloupe
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gravatar for rmf
8 weeks ago by
rmf • 1.1k
rmf • 1.1k wrote:

I have my data as "10x" format.

barcodes.tsv
genes.tsv
matrix.mtx

How can I convert this to .cloupe format to view in the 10x loupe browser?
transcriptomics single-cell 10x • 184 views
ADD COMMENT • link •
modified 8 weeks ago by swbarnes2 ♦ 9.6k • written 8 weeks ago by rmf • 1.1k

The .cloupe file contains additional information that is not available in those three files, so it would not be possible to convert them.

ADD REPLY • link written 8 weeks ago by igor ♦ 12k
1
gravatar for swbarnes2
8 weeks ago by
swbarnes2 ♦ 9.6k
United States
swbarnes2 ♦ 9.6k wrote:

I asked 10x once...you can't. You need to run cellranger on the fastqs to make a loupe file.
ADD COMMENT • link written 8 weeks ago by swbarnes2 ♦ 9.6k

Hmm.. Someone needs to reverse engineer the .cloupe format :) https://github.com/10XGenomics/cellranger/blob/master/mro/stages/cloupe/cloupe_preprocess/__init__.py

ADD REPLY • link written 8 weeks ago by rmf • 1.1k
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