exportPhasedReads: Export Strand-seq phased reads in FASTA or FASTQ format.

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

Export Strand-seq phased reads in FASTA or FASTQ format.

Description

This function will take phase information for each single cell and each haplotype informative region and will divide all mapped reads in BAM format into haplotype specific sets. In case of paired-end reads, read1 and read2 will be exported in separate files.

Usage

exportPhasedReads(
  phased.tab = NULL,
  inputfolder = NULL,
  outputfolder = NULL,
  by.matepair = TRUE,
  min.mapq = 10,
  pairedEndReads = TRUE,
  format = "fastq"
)

Arguments

phased.tab	A data table containing haplotype assignment for each single cell and haplotype informative region. This table is standard output of StrandPhaseR and cen be found in subfolder 'Phased/phased_haps.txt'.
inputfolder	Path to the bam files to process
outputfolder	Output directory. If non-existent it will be created.
by.matepair	If set to TRUE (the default) paired-end reads will be exported per mate-pair (read1 and read2).
min.mapq	Minimum mapping quality when importing from BAM files.
pairedEndReads	Set to TRUE if you have paired-end reads in your file.
format	User defined output format, either "fasta" or "fastq" (the default).

Author(s)

David Porubsky

daewoooo/StrandPhaseR documentation built on April 7, 2024, 7:13 p.m.