How to convert 10x matrix.mtx.gz files to hdf5 format?

Question

[johnny rocketfingers]

I have a bunch of folders containing barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz from the Cellranger Count output for a single-cell dataset that was sent to me from another lab. I need the .h5 version of these count matrices, but I do not have access to the original Cellranger Count output which contains the generated .h5 files.

Is there an R or Python function that can reliably convert these files into the proper hdf5 format? I haven't found anything online yet.

x-post:

• https://www.reddit.com/r/bioinformatics/comments/veku5r/how_to_convert_10x_matrix_tsv_files_to_hdf5_format (reddit)
• https://bioinformatics.stackexchange.com/questions/19263/how-to-convert-10x-matrix-mtx-gz-files-to-hdf5-format (stackexchange)

[Ram]

Do not shotgun post on multiple fora. It is bad etiquette.

Answer 1

[ATpoint]

https://rdrr.io/github/MarioniLab/DropletUtils/man/write10xCounts.html