What it does

Kallisto and Alevin (and possibly other tools) output an MTX file and associated labels that are not consistent with the old-style 10X, meaning that routines designed to parse those files cannot be used. This tool transforms (in the mathematical sense) the matrix, and reformats the genes file (essentially duplicating the column) to match those earlier conventions.

Inputs

MTX and row and gene labels from the relevant tool. For Alevin this will be

• Matrix file: quants_mat.mtx.gz
• Genes file: quants_mat_cols.txt
• Barcodes file: quants_mat_rows.txt

For Kallisto it will be:

• Matrix file: [name].mtx.gz
• Genes file: [name].genes.txt
• Barcodes file: [name].barcodes.txt

Outputs

• MTX, gene and cell labels in 10X style