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.
Please note the cell IDs (column names) are availible in the "matrix.cells" file generated by kallisto "pseudo".