reczko@max:/data/images/proton/run290$ ../rnaSeq-pip6fast-mm10.sh 
reczko@estia:/data/images/proton/run291/www$ ln -s ../../run291/tophat_003/sort_uniq.bam IPR24-LIVE.bam
reczko@estia:/data/images/proton/run291/www$ ln -s ../../run291/tophat_004/sort_uniq.bam IPR25-fINV2.bam
reczko@estia:/data/images/proton/run291/www$ ln -s ../../run291/tophat_005/sort_uniq.bam IPR26-fINV1.bam
reczko@estia:/data/images/proton/run291/www$ ln -s ../../run290/tophat_006/sort_uniq.bam IPR27-FixedA.bam
reczko@estia:/data/images/proton/run291/www$ ln -s ../../run290/tophat_007/sort_uniq.bam IPR28-FixedB.bam
reczko@estia:/data/images/proton/run291/www$ ln -s ../../run290/tophat_008/sort_uniq.bam IPR29-NGSFixed.bam


metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("LiveInv_vs_FIXED"),
    org="mm10",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_run291"),
    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","flags"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    count.type="exon",
    restrict.cores=0.3,
fig.format=c("png","pdf")
)


# tracks
reczko@max:/data/images/proton/run291/www$ grep -H Inp /data/images/proton/run29[0,1]/tophat_0*/align_summary.txt 
/data/images/proton/run290/tophat_006/align_summary.txt:          Input     :  24160136
/data/images/proton/run290/tophat_007/align_summary.txt:          Input     :  24251325
/data/images/proton/run290/tophat_008/align_summary.txt:          Input     :  25136547
/data/images/proton/run291/tophat_003/align_summary.txt:          Input     :  22816987
/data/images/proton/run291/tophat_004/align_summary.txt:          Input     :  28704023
/data/images/proton/run291/tophat_005/align_summary.txt:          Input     :  27198996
ls -l *bam
lrwxrwxrwx 1 reczko users 37 Jun 14 14:48 IPR27-FixedA.bam -> ../../run290/tophat_006/sort_uniq.bam
lrwxrwxrwx 1 reczko users 37 Jun 14 14:49 IPR28-FixedB.bam -> ../../run290/tophat_007/sort_uniq.bam
lrwxrwxrwx 1 reczko users 37 Jun 14 14:49 IPR29-NGSFixed.bam -> ../../run290/tophat_008/sort_uniq.bam
lrwxrwxrwx 1 reczko users 37 Jun 14 14:51 IPR24-LIVE.bam -> ../../run291/tophat_003/sort_uniq.bam
lrwxrwxrwx 1 reczko users 37 Jun 14 14:51 IPR25-fINV2.bam -> ../../run291/tophat_004/sort_uniq.bam
lrwxrwxrwx 1 reczko users 37 Jun 14 14:51 IPR26-INV1.bam -> ../../run291/tophat_005/sort_uniq.bam

=> reads.txt
IPR27-FixedA.bam     24160136
IPR28-FixedB.bam     24251325
IPR29-NGSFixed.bam   25136547
IPR24-LIVE.bam	     22816987
IPR25-fINV2.bam	     28704023
IPR26-INV1.bam	     27198996

sampled to smallest library IPR24-LIVE.bam with 22816987 reads

reczko@max:/data/images/proton/run291/www$ awk -f ../../make-stranded-sampled-mm10-tracks1.awk  reads.txt  > make-stranded-sampled-mm10-tracks.sh
reczko@max:/data/images/proton/run291/www$ chmod a+x *sh
reczko@max:/data/images/proton/run291/www$ ./make-stranded-sampled-mm10-tracks.sh