require(metaseqR)
the.path="/data/images/proton/run332/www"
metaseqr(
    sample.list=file.path(the.path,"targets2.txt"),
    contrast=c("wtBr_vs_koBr","wtEu_vs_koEu","wtBr_vs_wtEu","koBr_vs_koEu"),
    org="mm10",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_run332"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,
    export.what=c("annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)