pileup_by_QUAL: Pileup by QUAL

In rocioespci/single: Accurate consensus sequence from nanopore reads of a gene library

Pileup by QUAL

Description

To explain

Usage

pileup_by_QUAL(
  bam_file,
  QUAL_values = seq(93, 0),
  pos_start = NA,
  pos_end = NA
)

Arguments

bam_file	Bam file to pile up
QUAL_values	Numeric vector. QUAL values to analyze in the data.
pos_start	Numeric. Position to start analyzing, counting starts from 1 and it refers to reference used for minimap2 alignment.
pos_end	Numeric. Position to stop analyzing, counting starts from 1 and it refers to reference used for minimap2 alignment.

Value

data.frame with columns strand,pos,nucleotide,QUAL,countss

Examples

refseq_fasta <- system.file("extdata", "ref_seq.fasta", package = "single")
train_reads_example <- system.file("extdata", "train_seqs_500.sorted.bam",
                                   package = "single")
counts_pnq <- pileup_by_QUAL(bam_file=train_reads_example,
    pos_start=1,pos_end=10)
head(counts_pnq)

rocioespci/single documentation built on April 18, 2023, 8:48 p.m.