Umi-collapser

Description

Umi-collapser identifies families of molecules in scRNA-seq experiments originating from the same original molecule and merges them into a single output read, calling consensus bases for any bases covered by multiple reads

Consensus base calling

Two methods of consensus bases calling are currently supported: calculation of the posterior probabilities for each base and simple majority voting.

Inputs and Output

Umi-collapser accepts a BAM files with reads tagged by cellular and molecular barcodes and outputs a new BAM file where reads from the same family are collapsed. Reads that do not form families of more than one are output with no modification.

Example Usage

$ umi-collapser --help
usage: umi-collapser [-h] -i INPUT_BAM -o OUTPUT_BAM [--input_is_sorted]
                   [--cell_barcode_tag CELL_BARCODE_TAG]
                   [--molecular_barcode_tag MOLECULAR_BARCODE_TAG]
                   [--gene_tag GENE_TAG]
                   [--calling_method {posterior,majority}] [--verbose]
                   [--debug]

Collapse reads from the same Gene, UMI, Cell Barcode Triplet

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT_BAM, --input_bam INPUT_BAM
                        input bamfile
  -o OUTPUT_BAM, --output_bam OUTPUT_BAM
                        output bamfile
  --input_is_sorted     flag indicating if the input bam is sorted by tags
  --cell_barcode_tag CELL_BARCODE_TAG
                        tag name for the cell barcode
  --molecular_barcode_tag MOLECULAR_BARCODE_TAG
                        tag name for the molecular barcode
  --gene_tag GENE_TAG   tag name for the gene tag
  --calling_method {posterior,majority}
                        method to use to call individual bases
  --verbose             verbosity level
  --debug               flag for debug mode

Ubuntu Installation

sudo apt-get install build-essential
sudo apt-get install libbz2-dev libcurl4-openssl-dev libssl-dev
python3 setup.py install