awk -v p="/data/images/proton/run326" -f ../../link-bam-files-to-sample-ids1.awk samples.txt > make-links.sh

awk -f /data/images/proton/make-stranded-sampled-mm10-tracks1.awk reads.txt > make-stranded-sampled-mm10-tracks2.sh

ln -s /data/images/proton/run326/tophat_003/sort_uniq.bam GSR13-KPM3.bam 
ln -s /data/images/proton/run326/tophat_004/sort_uniq.bam GSR14-KPM4.bam 
ln -s /data/images/proton/run325/tophat_002/sort_uniq.bam GSR12-KPM1.bam 
ln -s /data/images/proton/run325/tophat_001/sort_uniq.bam GSR11-wt1.bam

library(metaseqR)

the.path <- "/data/images/proton/run326/www/metaseqr_WT_vs_KPM"

the.contrasts.1 <- c(
	"WT_vs_KPM"
)

metaseqr(
    sample.list=file.path(the.path,"../targets.txt"),
    contrast=the.contrasts.1,
    annotation="download",
    org="mm10",
    normalization="deseq",
    statistics="deseq",
    fig.format=c("png","pdf"),
    export.where=the.path,
    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","mm10")
    ),
    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
)