splitReads: This will take phased info for each haplotype and will split...

In daewoooo/StrandPhaseR: Phase template strands from Strand-seq data

This will take phased info for each haplotype and will split directional reads of each single cell into haplotype specific reads

Description

This will take phased info for each haplotype and will split directional reads of each single cell into haplotype specific reads

Usage

splitReads(
  data.object = NULL,
  inputfolder = inputfolder,
  pairedEndReads = FALSE,
  min.mapq = 10,
  filterAltAlign = TRUE
)

Arguments

data.object	containing sorted and filtered watson and crick haplotypes of each single cell along with phase info
inputfolder	Path to the bam files to process
pairedEndReads	Set to TRUE if you have paired-end reads in your file.
min.mapq	Minimum mapping quality when importing from BAM files.

Author(s)

David Porubsky

daewoooo/StrandPhaseR documentation built on Jan. 17, 2025, 7:44 a.m.