A complete chipseq pipeline from fastq to MACS and Scripture
1 2 3 4 5 6 7 8 9 10 | 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")
|
fqs |
a character vector of paths to fastqs for a sample |
samplename |
name of this sample (a character vector, length one.) |
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