../rnaSeq-pip7fast-hg19-no-mRNA-build.sh
mkdir www
cd www
awk -f /data/images/proton/make-metaseqr-targets1.awk ../samples.txt > targets.txt
/data/images/proton/make-bam-links-tophat2.sh
source make-links.sh 
awk -f /data/images/proton/make-stranded-sampled-hg19-tracks1.awk reads.txt > make-stranded-sampled-hg19-tracks.sh

require(metaseqR)

the.contrasts=c(
"siLusi_vs_siLusiBAF",
"siLusi_vs_siApo",
"siLusi_vs_siApoBAF",
"siLusiBAF_vs_siApo",
"siLusiBAF_vs_siApoBAF",
"siApo_vs_siApoBAF")

the.path="/data/images/proton2/run419/www"
metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=the.contrasts,
    annotation="download",
    org="hg19",
    count.type="utr",
    normalization="deseq",
    statistics="deseq",
    fig.format=c("png","pdf"),
    export.where=file.path(the.path,"metaseqr_run419"),
    restrict.cores=0.5,
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise","filtered",
        "correl","pairwise","boxplot","gcbias","lengthbias","meandiff",
        "meanvar","biodist","volcano","deheatmap"
    ),
    exon.filters=NULL,
    gene.filters=list(
       length=list(
            length=500
        ),
        avg.reads=list(
            average.per.bp=100,
            quantile=0.25
        ),
        expression=list(
            median=TRUE,
            mean=FALSE,
            quantile=NA,
            known=NA,
            custom=NA
        ),
        biotype=get.defaults("biotype.filter","hg19")
    ),
    pcut=0.05,
    export.what=c("annotation","p.value","adj.p.value","fold.change",
		"counts","flags"),
    export.scale=c("log2","rpgm"),
    export.values="normalized",
    export.counts.table=TRUE,
	report.top=0.05
)