mutateReads: Randomly mutate read sequences

In tanaylab/reputils: Utility functions for working with transposable elements

Description

Introduces random mutations in read sequences given a specified error rate. Useful to simulate read mismapping under given error constrains.

Usage

mutateReads(BSgenome = NULL, reads, tes = NULL, paired = NULL,
  n_reads = NULL, outdir = NULL, prefix = "aligned_reads",
  which = GRanges(), error_rate = NULL, seed = 19)

Arguments

BSgenome	BSgenome. BSgenome to query sequences, e.g. Hsapiens.
tes	GRanges. GRanges object containing TE coordinates
outdir	Character. Specifies where to store output fastq files. If NULL (the default), same directory as input bam file.
bam_path	Character. Path to input BAM file.
multi_mapper	Logical. if FALSE (currently only supported), throws reads mapping to multiple position in the genome (NH:i tag).

Value

Returns GRanges object containing seqs column

tanaylab/reputils documentation built on Nov. 5, 2019, 9:58 a.m.