reczko@fix:/data/images/proton2/run403$ ../rnaSeq-pip6fast-mm10.sh
./pip.sh &> pip.log &
awk -f /data/images/proton/link-bam-files-to-sample-ids1.awk ../samples.txt > link-bam-files-to-sample-ids1.sh
source link-bam-files-to-sample-ids1.sh
awk -f /data/images/proton/make-metaseqr-targets1.awk ../samples.txt > targets.txt

require(metaseqR)
the.path <- "/data/images/proton2/run403/www"
the.contrasts.1 <- c(
	"Wt_vs_C_221_222",
	"Wt_vs_Tg197",
	"Tg197_C_vs_Tg197",
	"Tg197_C_vs_C_221_222"
)

#v2
metaseqr(
    sample.list=file.path(the.path,"targets-wo-GK3R197.txt"),
    contrast=the.contrasts.1,
    annotation="download",
    org="mm10",
    count.type="utr",
    normalization="deseq",
    statistics="deseq",
    fig.format=c("png","pdf"),
    export.where=file.path(the.path,"metaseqr_GKlab_run403-wo-GK3R197"),
    restrict.cores=0.5,
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise","filtered",
        "correl","pairwise","boxplot","gcbias","lengthbias",
        "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
)

#v1
metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=the.contrasts.1,
    annotation="download",
    org="mm10",
    count.type="utr",
    normalization="deseq",
    statistics="deseq",
    fig.format=c("png","pdf"),
    export.where=file.path(the.path,"metaseqr_GKlab_run403"),
    restrict.cores=0.5,
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise","filtered",
        "correl","pairwise","boxplot","gcbias","lengthbias",
        "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
)