dynast.consensus

Module Contents

Functions

consensus(bam_path: str, gtf_path: str, out_dir: str, strand: typing_extensions.Literal[forward, reverse, unstranded] = 'forward', umi_tag: Optional[str] = None, barcode_tag: Optional[str] = None, gene_tag: str = 'GX', barcodes: Optional[List[str]] = None, quality: int = 27, add_RS_RI: bool = False, n_threads: int = 8, temp_dir: Optional[str] = None)

Main interface for the consensus command.

dynast.consensus.consensus(bam_path: str, gtf_path: str, out_dir: str, strand: typing_extensions.Literal[forward, reverse, unstranded] = 'forward', umi_tag: Optional[str] = None, barcode_tag: Optional[str] = None, gene_tag: str = 'GX', barcodes: Optional[List[str]] = None, quality: int = 27, add_RS_RI: bool = False, n_threads: int = 8, temp_dir: Optional[str] = None)

Main interface for the consensus command.

Parameters

bam_path

Path to BAM to call consensus from

gtf_path

Path to GTF used to build STAR index

out_dir

Path to output directory

strand

Strandedness of the protocol

umi_tag

BAM tag to use as UMIs

barcode_tag

BAM tag to use as cell barcodes

gene_tag

BAM tag to use as gene assignments

barcodes

Only consider these barcodes

quality

Quality threshold

add_RS_RI

Add RS and RI tags to BAM. Mostly useful for debugging.

n_threads

Number of threads to use

temp_dir

Temporary directory