chipseq: A complete chipseq pipeline from fastq to MACS and Scripture

Description Usage Arguments

Description

A complete chipseq pipeline from fastq to MACS and Scripture

Usage

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chipseq(fqs, samplename = "sample_name", out_path,
  deffile = system.file("data/chipseq.def", package = "SaturnV"),
  bowtie_exe = "/risapps/rhel6/bowtie/1.1.2/bowtie",
  java_exe = "/risapps/noarch/jdk/jdk1.8.0_45/bin/java",
  igvtools_exe = "/rsrch2/genomic_med/krai/apps/igvtools/default/igvtools.jar",
  scripture_exe = "/rsrch2/genomic_med/krai/apps/scripture/scripture-beta2.jar",
  macs14_exe = "macs14",
  bowtie_index = "/rsrch2/genomic_med/krai/annot/indexes/bowtie/hg19",
  hg19table = "/rsrch2/genomic_med/krai/annot/hg19.table", chr_prefix = "",
  peak_fdr = "0.05")

Arguments

fqs

a character vector of paths to fastqs for a sample

samplename

name of this sample (a character vector, length one.)


flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.