import_files: Extract informative reads for insertion inference

In ctl43/TranSpotteR: Pipeline for identifying LINE1 insertoin in the WGS data

Extract informative reads for insertion inference

Description

Extract discordant reads and reads mapped to sequence in interest.

Usage

import_files <- function(extracted, seq_info)

Arguments

extracted	Paths to all reads extracted from extract_reads. The number of paths can be more than 1.
seqinfo	A Seqinfo object containing the chromosome information. It can be converted from a chrom_sizes.txt file, retrieved from sam/bam header or retrieved from R packages directly, e.g. BSgenome.

Details

All extract data are imported into the R system.

Value

A text file containing extracted reads. The text file is basically simplified sam format, which contains the fields of QNAME, FLAG, RNAME, POS, MAPQ, CIGAR, SEQUENCE and QNAME_id.

Author(s)

Cheuk-Ting Law

Examples

# For hs37d5,
library(BSgenome.Hsapiens.1000genomes.hs37d5)
seq_info <- seqinfo(hs37d5)
import_files("my_extract.txt", seq_info)

ctl43/TranSpotteR documentation built on Sept. 9, 2022, 5:49 p.m.