tidesurf.counter.UMICounter

class tidesurf.counter.UMICounter(transcript_index: TranscriptIndex, orientation: Literal['sense', 'antisense'], min_intron_overlap: int = 5, multi_mapped_reads: bool = False)

Bases: object

Counter for unique molecular identifiers (UMIs) with reads mapping to transcripts in single-cell RNA-seq data.

Parameters:

transcript_index TranscriptIndex

Transcript index.

orientation Literal['sense', 'antisense']

Orientation in which reads map to transcripts.

min_intron_overlap int

Minimum overlap of reads with introns required to consider them intronic (default: 5).

multi_mapped_reads bool

Whether to count multi-mapped reads (default: False).

Attributes

MIN_INTRON_OVERLAP	Minimum overlap of reads with introns required to consider them intronic.
multi_mapped_reads	Whether to count multi-mapped reads.
orientation	Orientation in which reads map to transcripts.
transcript_index	Transcript index for extraction of overlapping transcripts.

Methods

count(bam_file[, filter_cells, whitelist, ...])

Count UMIs with reads mapping to transcripts.