the.path <- "~/run_429_430"
the.contrasts.1 <- c(
	"Wt-4w-SP_vs_Tg-4w-SP",
	"Wt-4w-DP_vs_Tg-4w-DP",
	"Wt-8w-SP_vs_Tg-8w-SP",
	"Wt-8w-DP_vs_Tg-8w-DP",
	"Wt-12w-SP_vs_Tg-12w-SP",
	"Wt-12w-DP_vs_Tg-12w-DP"
)

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_run429_430_431"),
    restrict.cores=0.5,
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise","filtered",
        "correl","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","mm10")
    ),
    pcut=0.05,
    export.what=c("annotation","p.value","adj.p.value","fold.change",
		"counts","flags"),
    export.scale=c("natural","log2","rpgm"),
    export.values="normalized",
    export.counts.table=TRUE,
	report.top=0.05
)