FastqToBam: Trims and maps reads based on Rbowtie2

In CL-CHEN-Lab/User_interface_for_Kronos_scRT: R-package and Shiny App interface for the analysis of single cell replication timing data

Trims and maps reads based on Rbowtie2

Description

Trims and maps reads based on Rbowtie2

Usage

FastqToBam(
  bowtie2_index,
  File1,
  File2 = NULL,
  adapters_list = NULL,
  outputdir = file.path(getwd(), "FastqToBam"),
  cores = 1,
  trim = T,
  phred33 = T,
  Read_min_size_after_trimming = 25
)

Arguments

bowtie2_index,	path to bowtie2 index
File1,	list of paths to fastq files (R1 files for PE)
File2,	list of paths to R2 fastq files for PE
adapters_list,	list of adapters to trim, if not provided general illumina adaters will be used
outputdir,	output path
cores,	number of parallel jobs
trim,	logical value, if False reads won't be trimmed
phred33,	logical value, if False phred64 will be used
Read_min_size_after_trimming,	read minimum size to be kept

CL-CHEN-Lab/User_interface_for_Kronos_scRT documentation built on Aug. 1, 2022, 2:08 p.m.