intSite: Fetch the integration sites from raw fastq files

In Heath1210/intSiteR: Process fastq files to get precise integration site coordinates

Description

This package integrated mergeReads, intTrim, alignBowtie2, sam2bam, bam2bed and intBed functions in this package, is used for a complete processing from raw fastq to integration site coordinates. Alternatively, you can also analysis your data step by step by separately using above mentioned functions, in such way you can tune lots of parameters to achieve better performance.

Usage

intSite(
  input,
  ref,
  bowtie2 = "bowtie2",
  samtools = "samtools",
  bedtools = "bedtools",
  mode = "file",
  theta = 100,
  fThreshold = 5,
  monoSite = 50,
  collapse = 7,
  mixBarcode = FALSE
)

Arguments

input	a folder containing raw fastq files
ref	genome reference for bowtie2, including file path and file prefix
bowtie2	path to bowtie2
samtools	path to samtools
bedtools	path to bedtools
mode	output mode, whether by file type or by sample, value can be 'file' or 'sample', default by file type.
theta	a parameter controlling the looseness of filter by duplicate degree, default is 100. Choose a bigger value if you want it to be looser, vice versa.
fThreshold	the minimum duplicate degree allowed for further analysis, default is 5.
monoSite	a threshold that insiteCode with frequency above it will not be filtered by breaking point, default is 50.
collapse	how close the neighboring sites will collapsed to one, default is 7.
mixBarcode	whether samples with different barcodes mixed in one library, default is false.

Author(s)

Cai Haodong

Examples

if(FALSE){
  dir.create('~/intTest')

  file.copy(from = system.file('extdata','raw',package = 'intSiteR'),
            to = '~/intTest',
            recursive = TRUE)

  intSite(input = '~/intTest/raw',
          ref = '~/Homo_sapiens.GRCh38', # change to your bt2 reference
          mode = 'sample')
 }

Heath1210/intSiteR documentation built on Dec. 17, 2021, 10:32 p.m.