Use this tool to convert the output of kallisto pseudo into a equivalence class counts matrix suitable for input into Seurat.
This tool was created because I was unable to extract a Seurat compatable expression matrix from the output of kallisto "pseudo". It relies on modified version of the "prep_TCC_matrix.py" script written by the pachterlab https://github.com/pachterlab/scRNA-Seq-TCC-prep
Example usage is as follows:
python3 prep_TCC_matrix.py -T matrix.tsv -E matrix.ec -O outputDir -I Mus_musculus.GRCm38.cdna.all.fa
-E | --inputMatrixec # Provide the "matrix.ec" file output by kallisto "pseudo"
-T | --inputMatrixtsv # Provide the "matrix.tsv" file output by kallisto "pseudo"
-O | --outputDir # Provide the path to your desired output directory
-I | --indexFasta # Provide the path to the index .fasta file that was used to generate your kallisto .idx file. This file must be unzipped
The output of this script is three files.
- The expression matrix table.
- The row names (Equivalence class IDs)
- A mapping of the Equivalence class ID to corresponding transcript IDs
Please note the cell IDs (column names) are availible in the "matrix.cells" file generated by kallisto "pseudo".