dynast.count
Module Contents
Functions
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Main interface for the count command. |
- dynast.count.count(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, control: bool = False, quality: int = 27, conversions: FrozenSet[FrozenSet[str]] = frozenset({frozenset({'TC'})}), snp_threshold: Optional[float] = None, snp_min_coverage: int = 1, snp_csv: Optional[str] = None, n_threads: int = 8, temp_dir: Optional[str] = None, velocity: bool = True, strict_exon_overlap: bool = False, dedup_mode: typing_extensions.Literal[auto, exon, conversion] = 'auto', by_name: bool = False, nasc: bool = False, overwrite: bool = False)[source]
Main interface for the count command.
- Parameters
- bam_path
Path to BAM
- gtf_path
Path to GTF
- out_dir
Path to output directory
- strand
Strandedness of technology
- umi_tag
BAM tag to use as UMIs
- barcode_tag
BAM tag to use as barcodes
- gene_tag
BAM tag to use as genes
- barcodes
List of barcodes to consider
- control
Whether this is a control sample
- quality
Quality threshold in detecting conversions
- conversions
Set of conversions to quantify
- snp_threshold
Call genomic locations that have greater than this proportion of specific conversions as a SNP
- snp_min_coverage
Only consider genomic locations with at least this many mapping reads for SNP calling
- snp_csv
CSV containing SNPs
- n_threads
Number of threads to use
- temp_dir
Temporary directory
- velocity
Whether to quantify spliced/unspliced RNA
- strict_exon_overlap
Whether spliced/unspliced RNA quantification is strict
- dedup_mode
UMI deduplication mode
- by_name
Whether to group counts by gene name instead of ID
- nasc
Whether to match NASC-seq pipeline behavior
- overwrite
Overwrite existing files