/data/results/reference/bacteria/PseudomonasAeruginosa/build-bowtie2-indices.sh

pipDME.sh &> pipDME.log

reczko@max:/data/images/proton2/run347/wwwDrApidianakis$ awk -f ../../link-bam-files-to-sample-ids1.awk ../samples-dme.txt 
awk -f ../../link-bam-files-to-sample-ids1.awk ../samples-dme.txt 
ln -s /data/images/proton2/run347/tophat_003/sort_uniq.bam YAbR21-OD3-B133-3.bam
ln -s /data/images/proton2/run347/tophat_005/sort_uniq.bam YAbR24-OD3-C3719-3.bam
ln -s /data/images/proton2/run347/tophat_025/sort_uniq.bam YA3R1-Byn1.bam
ln -s /data/images/proton2/run347/tophat_026/sort_uniq.bam YA3R2-Byn2.bam
ln -s /data/images/proton2/run347/tophat_027/sort_uniq.bam YA3R3-Byn3.bam
ln -s /data/images/proton2/run347/tophat_028/sort_uniq.bam YA3R4-BynRas1.bam
ln -s /data/images/proton2/run347/tophat_029/sort_uniq.bam YA3R5-BynRas2.bam
ln -s /data/images/proton2/run347/tophat_030/sort_uniq.bam YA3R6-BynRas3.bam


awk -f /data/images/proton/make-stranded-sampled-dme-tracks1.awk reads-dme.txt > make-tracks.sh
reczko@max:/data/images/proton2/run347/wwwDrApidianakis$ source !$
source make-tracks.sh
# purge hub cache
# http://genome.ucsc.edu/cgi-bin/hgTracks?udcTimeout=1& (with the remainder of the URL following the ampersand)
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?udcTimeout=1&db=dm6&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr2L%3A1%2D341879&hgsid=1675_yK4K2tAcXmvj4DFv7sJVdoMD3kIu

awk -f /data/images/proton/make-metaseqr-targets1.awk ../samples-dme.txt > targets.txt

reczko@max:/data/images/proton2/run347/wwwDrApidianakis$ for i in *bam
for i in *bam
do
/data/results/tools/proton/addChrToBam.sh $i $i".chr.bam"
echo $i
done
#edit targets.txt, add ".chr.bam"

the.path="/data/images/proton2/run347/wwwDrApidianakis"
metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast="Byn_vs_Ras",
    annotation="download",
    org="dm6",
    count.type="utr",
    normalization="edger",
    statistics="edger",
#    normalization="deseq",
#    statistics="deseq",
    fig.format=c("png","pdf"),
    export.where=file.path(the.path,"metaseqr_Apidianakis_run347"),
    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=100
        ),
        avg.reads=list(
            average.per.bp=10,
            quantile=0.1
        ),
        expression=list(
            median=FALSE,
            mean=FALSE,
            quantile=NA,
            known=NA,
            custom=NA
        ),
        biotype=get.defaults("biotype.filter","hg19")
    ),
    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
)