Skip to contents

convert_mtx_to_h5: Converts the triple .mtx files from single cell experiments to a .h5 counts file

convert_mtx_to_h5.Rd

Uses existing tools to generate .h5 files, which can be easier to import or transfer

Usage

convert_mtx_to_h5(sample_name, mtx_file, features_file, barcodes_file)

Arguments

sample_name

A character string to be used to name the sample

mtx_file

Path to the matrix.mtx.gz file

features_file

Path to the features.tsv.gz file

barcodes_file

Path to the barcodes.tsv.gz file

Details

Older versions of CellRanger, in addition to some other single cell alignment tools, such as PipSeq and DropSeq, produce a trio of files in an output director that pointed to all the necessary features:

  • matrix.mtx.gz: A matrix counts file with cells in the columns and features in the rows

  • barcodes.tsv.gz: A tab-separated file with cell/droplet barcode sequences

  • features.tsv.gz: A tab-separated file with gene names (or other features)