FULA 1 IonXpressRNA_004 run184/R_2015_05_14_12_15_30_user_ION-184-DrStathopoulos_150514_NKRNAseq_GSR1-4.GSR1-FULA1.IonXpressRNA_004.fastq
BULA 1 IonXpressRNA_011 run184/R_2015_05_14_12_15_30_user_ION-184-DrStathopoulos_150514_NKRNAseq_GSR1-4.GSR4-BULA1.IonXpressRNA_011.fastq
BULA 2 IonXpressRNA_012 run185/R_2015_05_15_12_20_11_user_ION-185-DrStathopoulos_150515_NKRNAseq_GSR5-6.GSR5-BULA2.IonXpressRNA_012.fastq
BELA 1 IonXpressRNA_013 run185/R_2015_05_15_12_20_11_user_ION-185-DrStathopoulos_150515_NKRNAseq_GSR5-6.GSR6-BELA1.IonXpressRNA_013.fastq
FULA 2 IonXpressRNA_006 run186/R_2015_05_21_11_36_50_user_ION-186-DrStathopoulos_150521_NKRNAseq_GSR2-7.GSR2-FULA1.IonXpressRNA_006.fastq
BELA 2 IonXpressRNA_014 run186/R_2015_05_21_11_36_50_user_ION-186-DrStathopoulos_150521_NKRNAseq_GSR2-7.GSR7-BELA2.IonXpressRNA_014.fastq
FULA 3 IonXpressRNA_010	run187/R_2015_05_22_13_04_56_user_ION-187-DrStathopoulos_150522_NKRNAseq_GSR3-8.GSR3-FULA3.IonXpressRNA_010.fastq
FVB Trachea IonXpressRNA_015 run187/R_2015_05_22_13_04_56_user_ION-187-DrStathopoulos_150522_NKRNAseq_GSR3-8.GSR8-FUBtrachea.IonXpressRNA_015.fastq
CULA IonXpress_016 run277/R_2016_03_08_13_22_40_user_IONAS-277-ITlab_DrStath_160308_ChIP-RNA_ITC112-113_GSR10.GSR10-P53FllFl.IonXpress_016.fastq
Balb/c IonXpressRNA_014_rawlib.basecaller  run268/R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSR9-mTECsBalbc.IonXpressRNA_014.fastq
The samples pending are FELA1 and FELA2.
So in total, we will have data on FULA cells (n=3), BULA cells (n=2), BELA cells (n=2), FELA cells
(n =2), CULA cells (n=1), and benign tracheal cells (n=2, one from each FVB and BALB/c strains,
samples FVB Trachea IonXpressRNA_015 and Balb/c IonXpressRNA_014_rawlib.basecaller).
The names of these cell lines have 4 parts: The first letter indicates the mouse strain of origin (C,
C57BL/6; F, FVB; B, Balb/c), the second the carcinogen used (U, urethane; E, DEN), LA denotes
lung adenocarcinoma, and the number their series of derivation from different mice.
The comparisons of gene expression we want to do are:
I) Each of the five different tumor cell categories compared with benign samples by unpaired
student's t-test and a cutoff of 2.
II) A comparison by strain, ie, FULA and FELA cells (n=5) compared with BULA and BELA cells
(n=4) of all genes and of only the genes emerging from I.
III) A comparison by carcinogen, ie, FULA and BULA and CULA cells (n=6) compared with FELA
and BELA cells (n=4) of all genes and of only the genes emerging from I.

reczko@max:/data/images/proton/StathopoulosLab/lung$ ../../rnaSeq-pip6fast-mm10.sh
reczko@max:/data/images/proton/StathopoulosLab/lung$ ./pip.sh &> pip.log &

#@ 3UTRseq
the.contrasts.1 <- c(
	"Benign_vs_FULA",
	"Benign_vs_BULA",
	"Benign_vs_BELA",
	"Benign_vs_CULA"
)

the.path="/data/images/proton/StathopoulosLab/lung/www"
metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=the.contrasts.1,
    annotation="download",
    org="mm10",
    refdb="refseq",
    normalization="deseq",
    statistics="deseq",
    fig.format=c("png","pdf"),
    export.where=file.path(the.path,"metaseqr_StathopoulosLab_lung"),
    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=500
        ),
        avg.reads=list(
            average.per.bp=100,
            quantile=0.25
        ),
        expression=list(
            median=TRUE,
            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
)

targets_carcinogen
FULAandBULAandCULA_vs_BELA

targets_strain
BULAandBELA_vs_FULA