10x to cloupe

Question

[firestar]

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?

[igor]

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

[jonas.andersson]

Anyone knows if something has happened here and made it possible somehow?

I would like to exclude features that are present in < 3 cells, this is possible in Seurat but not in Loupe browser. Does anyone know how to or if it is possible?

best Jonas

[Ram]

This was not an answer and should not have been added as one. I've moved it to a comment - please be more careful in the future.

Answer 1

[swbarnes2]

I asked 10x once...you can't. You need to run cellranger on the fastqs to make a loupe file.

[firestar]

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

Answer 2

[firestar]

Finally, it's here: loupeR.