/data/images/proton/rnaSeq-pip7fast-hg19-no-mRNA-build.sh

reczko@fix:/mnt/max/a/genomics_facility/proton3/run469$ ./pip.sh &> pip.log &
reczko@fix:/mnt/max/a/genomics_facility/proton3/run469$ awk -f /data/images/proton/link-bam-files-to-sample-ids1.awk samples.txt > make-links.sh

reczko@fix:/mnt/max/a/genomics_facility/proton3/run469$ reczko@fix:/mnt/max/a/genomics_facility/proton3/run469$ ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_011/sort_uniq.bam PMN5.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_015/sort_uniq.bam PMN9.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_016/sort_uniq.bam PMN10.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_037/sort_uniq.bam BMC3R1_M9wt1a.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_038/sort_uniq.bam BMC3R2_M10wt1b.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_039/sort_uniq.bam BMC3R3_M16wt2a.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_040/sort_uniq.bam BMC3R4_M17wt2b.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_041/sort_uniq.bam BMC3R5_M12tg1a.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_042/sort_uniq.bam BMC3R6_M13tg1b.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_043/sort_uniq.bam BMC3R7_M14tg1c.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_044/sort_uniq.bam BMC3R8_M15tg1d.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_045/sort_uniq.bam BMC3R9_M20tg2a.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_046/sort_uniq.bam BMC3R10_M21tg2b.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_047/sort_uniq.bam BMC3R11_M22tg2c.bam
ln -s /mnt/max/a/genomics_facility/proton3/run469/tophat_048/sort_uniq.bam BMC3R12_M23tg2d.bam

reczko@fix:/mnt/max/a/genomics_facility/proton3/run469$ awk -f /data/images/proton/make-metaseqr-targets1.awk samples.txt > targets.txt

reczko@fix:/mnt/max/a/genomics_facility/proton3/run469$ /data/results/tools/r/R-4.0.0/bin/R
library(metaseqR2)
the.path <- "/mnt/max/a/genomics_facility/proton3/run469"
the.contrasts.1 <- c(
	"wt_vs_tg1","wt_vs_tg2"
)

the.contrasts.2 <- c(
	"wt_vs_tg1"
)

the.contrasts.3 <- c(
	"wt_vs_tg2"
)

  result <- metaseqr2(
    #counts = "/home/tzanos/Desktop/HuR/gene_counts_merged_k20_mm10.txt",
    sampleList=file.path(the.path, "targets.txt"),
    #excludeList = c("KO01", "KO02", "KO21", "KO22", "KO61", "KO62", "wt01", "wt02", "wt21", "wt22", "wt61", "wt62"),
    fileType = "bam",
    contrast=the.contrasts.1,
    org="hg19",
#annotation="embedded",
localDb ="/data/results/tools/rnaseq/metaseqr/mm10/annotation.sqlite",
refdb = "ensembl",
    transLevel = "gene",
    countType="utr",
    normalization="deseq",
    statistics=c("deseq","deseq2","edger","noiseq","limma","nbpseq","absseq","dss"),
    adjustMethod = "fdr",
    metaP="pandora",
    figFormat=c("png","pdf", "jpg"),
    exportWhere=file.path(the.path, "metaseqR2_run469a"),
    restrictCores=0.5,
    qcPlots=c("mds","biodetection","countsbio","saturation","readnoise",
              "pairwise","filtered","correl","boxplot","meandiff",
              "meanvar","boxplot", "filtered", "biodist","volcano","mastat", "deheatmap"
              ),
    exonFilters=NULL,
    geneFilters=list(
      #length=list(length=500),
      avgReads=list(averagePerBp=100, quantile=0.25),
      expression=list(median=TRUE,
                     mean=FALSE,
                     quantile=NA,
                     known=NA,
                     custom=NA),
      biotype=getDefaults("biotypeFilter", "mm10"),
      presence = list(
        frac=0.5,
        minCount=1,
        perCondition=TRUE
      )
    ),
    #pcut=0.05,
    outList = TRUE,
    exportWhat=c("annotation","p_value","adj_p_value","meta_p_value",
                 "adj_meta_p_value","fold_change","stats","counts","flags"),
    exportScale=c("natural","log2","rpgm"),
    exportValues="normalized",
    exportStats = c("mean", "median", "sd", "mad", "cv"),
    exportCountsTable=TRUE,
    #reportTop=0.05,
    saveGeneModel = TRUE,
    createTracks=TRUE,
    overwrite=TRUE,
    trackInfo=list(
      stranded=TRUE,
      normTo=1e+8,
      #urlBase="http://epigenomics.fleming.gr/home/tzanos/public_html/DK/HuR/metaseqR2_DK_pandora_tracks/tracks",
      hubInfo=list(
        name="EDHub",
        shortLabel="ED Hub",
        longLabel="ED hub long",
        email="reczko@fleming.gr"
      )
    )
  )
  
  result <- metaseqr2(
    #counts = "/home/tzanos/Desktop/HuR/gene_counts_merged_k20_mm10.txt",
    sampleList=file.path(the.path, "targets2.txt"),
    #excludeList = c("KO01", "KO02", "KO21", "KO22", "KO61", "KO62", "wt01", "wt02", "wt21", "wt22", "wt61", "wt62"),
    fileType = "bam",
    contrast=the.contrasts.2,
    org="hg19",
#annotation="embedded",
localDb ="/data/results/tools/rnaseq/metaseqr/mm10/annotation.sqlite",
refdb = "ensembl",
    transLevel = "gene",
    countType="utr",
    normalization="deseq",
    statistics=c("deseq","deseq2","edger","noiseq","limma","nbpseq","absseq","dss"),
    adjustMethod = "fdr",
    metaP="pandora",
    figFormat=c("png","pdf", "jpg"),
    exportWhere=file.path(the.path, "metaseqR2_run469b"),
    restrictCores=0.5,
    qcPlots=c("mds","biodetection","countsbio","saturation","readnoise",
              "pairwise","filtered","correl","boxplot","meandiff",
              "meanvar","boxplot", "filtered", "biodist","volcano","mastat", "deheatmap"
              ),
    exonFilters=NULL,
    geneFilters=list(
      #length=list(length=500),
      avgReads=list(averagePerBp=100, quantile=0.25),
      expression=list(median=TRUE,
                     mean=FALSE,
                     quantile=NA,
                     known=NA,
                     custom=NA),
      biotype=getDefaults("biotypeFilter", "mm10"),
      presence = list(
        frac=0.5,
        minCount=1,
        perCondition=TRUE
      )
    ),
    #pcut=0.05,
    outList = TRUE,
    exportWhat=c("annotation","p_value","adj_p_value","meta_p_value",
                 "adj_meta_p_value","fold_change","stats","counts","flags"),
    exportScale=c("natural","log2","rpgm"),
    exportValues="normalized",
    exportStats = c("mean", "median", "sd", "mad", "cv"),
    exportCountsTable=TRUE,
    #reportTop=0.05,
    saveGeneModel = TRUE,
    createTracks=TRUE,
    overwrite=TRUE,
    trackInfo=list(
      stranded=TRUE,
      normTo=1e+8,
      #urlBase="http://epigenomics.fleming.gr/home/tzanos/public_html/DK/HuR/metaseqR2_DK_pandora_tracks/tracks",
      hubInfo=list(
        name="EDHub",
        shortLabel="ED Hub",
        longLabel="ED hub long",
        email="reczko@fleming.gr"
      )
    )
  )
  
  result <- metaseqr2(
    #counts = "/home/tzanos/Desktop/HuR/gene_counts_merged_k20_mm10.txt",
    sampleList=file.path(the.path, "targets3.txt"),
    #excludeList = c("KO01", "KO02", "KO21", "KO22", "KO61", "KO62", "wt01", "wt02", "wt21", "wt22", "wt61", "wt62"),
    fileType = "bam",
    contrast=the.contrasts.3,
    org="hg19",
#annotation="embedded",
localDb ="/data/results/tools/rnaseq/metaseqr/mm10/annotation.sqlite",
refdb = "ensembl",
    transLevel = "gene",
    countType="utr",
    normalization="deseq",
    statistics=c("deseq","deseq2","edger","noiseq","limma","nbpseq","absseq","dss"),
    adjustMethod = "fdr",
    metaP="pandora",
    figFormat=c("png","pdf", "jpg"),
    exportWhere=file.path(the.path, "metaseqR2_run469c"),
    restrictCores=0.5,
    qcPlots=c("mds","biodetection","countsbio","saturation","readnoise",
              "pairwise","filtered","correl","boxplot","meandiff",
              "meanvar","boxplot", "filtered", "biodist","volcano","mastat", "deheatmap"
              ),
    exonFilters=NULL,
    geneFilters=list(
      #length=list(length=500),
      avgReads=list(averagePerBp=100, quantile=0.25),
      expression=list(median=TRUE,
                     mean=FALSE,
                     quantile=NA,
                     known=NA,
                     custom=NA),
      biotype=getDefaults("biotypeFilter", "mm10"),
      presence = list(
        frac=0.5,
        minCount=1,
        perCondition=TRUE
      )
    ),
    #pcut=0.05,
    outList = TRUE,
    exportWhat=c("annotation","p_value","adj_p_value","meta_p_value",
                 "adj_meta_p_value","fold_change","stats","counts","flags"),
    exportScale=c("natural","log2","rpgm"),
    exportValues="normalized",
    exportStats = c("mean", "median", "sd", "mad", "cv"),
    exportCountsTable=TRUE,
    #reportTop=0.05,
    saveGeneModel = TRUE,
    createTracks=TRUE,
    overwrite=TRUE,
    trackInfo=list(
      stranded=TRUE,
      normTo=1e+8,
      #urlBase="http://epigenomics.fleming.gr/home/tzanos/public_html/DK/HuR/metaseqR2_DK_pandora_tracks/tracks",
      hubInfo=list(
        name="EDHub",
        shortLabel="ED Hub",
        longLabel="ED hub long",
        email="reczko@fleming.gr"
      )
    )
  )