samplename	filename	condition	paired	stranded
SCR20	/data/images/proton/run141/tophat_005/sort_uniq.bam	WT	single	yes
SCR21	/data/images/proton/run143/tophat_009/sort_uniq.bam	WT	single	yes
SCR22	/data/images/proton/run141/tophat_014/sort_uniq.bam	HET	single	yes
SCR23	/data/images/proton/run143/tophat_015/sort_uniq.bam	HET	single	yes

targets_run20.txt
samplename	filename	condition	paired	stranded
SCR1	/data/images/proton/run20/tophat_001/sort_uniq.bam	TR	single	yes
SCR2	/data/images/proton/run20/tophat_002/sort_uniq.bam	WT	single	yes

reczko@estia:/data/images/proton/run164$ /home/moulos/Rbase/bin/R
@@

the.path="/data/images/proton/run179/www"
metaseqr(
    sample.list=file.path(the.path,"targets-run179.txt"),
    contrast=c("CtrlSal_vs_TgSal"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_CtrlSal_vs_TgSal"),
    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")
)


the.path="/data/images/proton/run183/www"
metaseqr(
    sample.list=file.path(the.path,"targets-run183.txt"),
    contrast=c("CtrlArs_vs_TgArs"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_CtrlArs_vs_TgArs"),
    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")
)

metaseqr(
    sample.list=file.path(the.path,"targets-run183.txt2"),
    contrast=c("CtrlSal_vs_CtrlArs"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_CtrlSal_vs_CtrlArs_only"),
    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")
)

## added all samples:
metaseqr(
    sample.list=file.path(the.path,"targets-run183.txt"),
    contrast=c("CtrlSal_vs_CtrlArs"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_CtrlSal_vs_CtrlArs"),
    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")
)

metaseqr(
    sample.list=file.path(the.path,"targets-run183.txt"),
    contrast=c("TgSal_vs_TgArs"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_TgSal_vs_TgArs"),
    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")
)

the.path="/data/images/proton/run183/www"
metaseqr(
    sample.list=file.path(the.path,"targets-run183.txt"),
    contrast=c("CtrlArs_vs_TgArs"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_CtrlArs_vs_TgArs_all"),
    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")
)