Python package for generating hash tag oligo count matrices for demultiplexing cellranger output
Project description
counhto
An easy to use tool to count hashtag oligos (HTOs) from 10x cellranger count output processed with Antibody Captures for sample multiplexing
Install
The most convenient and easy way to install the package is
pip install countho
alternatively you could also clone the repository and install it manually like
git clone git@github.com:dmalzl/counhto.git
cd countho
pip install .
Usage
Using it is as simple as setting up a csv file with the following structure
bamfile | barcodefile | htofile | outputdir |
---|---|---|---|
cellranger/outs/possorted_bam.bam | cellranger/outs/filtered_feature_bc_matrix/barcodes.tsv.gz | cellranger/outs/feature_ref.csv | /path/to/outputdir/ |
cellranger/outs/possorted_bam.bam | cellranger/outs/filtered_feature_bc_matrix/barcodes.tsv.gz | cellranger/outs/feature_ref.csv | /path/to/outputdir/ |
and invoking countho as follows
countho --csv sample_csv.csv [-p n]
The -p
argument specifies the number of cpus to use for processing however this only has an effect if more than one samples are supplied.
The output for each sample will then be written to the specified output directories and will have the following structure
/path/to/outputdir/
|__
|__barcodes.tsv # filtered barcodes
|__features.tsv # names of the HTOs as specified in the feature_ref.csv file
|__matrix.mtx # MatrixMarket formated count matrix of shape n_barcodes x n_HTOs
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