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paulranum11 / kallisto_pseudo_to_expressionMatrix

Convert the output of kallisto "pseudo" to a expression matrix
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kallisto_pseudo_to_expressionMatrix

Use this tool to convert the output of kallisto pseudo into a equivalence class counts matrix suitable for input into Seurat.

About

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

Usage

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

Options

-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

Output

The output of this script is three files.

  1. The expression matrix table.
  2. The row names (Equivalence class IDs)
  3. 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".