anchor.diff:  
   // INPUT DATA
   
  -geneanno = 'BDGP6/Annotation/Genes/genes.gtf';
  -
  -fa = 'BDGP6/Sequence/WholeGenomeFasta/genome.fa';
  -fai = 'BDGP6/Sequence/WholeGenomeFasta/genome.fa.fai';
  -
  -idx = 'BDGP6/Sequence/BowtieIndex/genome.1.ebwt' 'BDGP6/Sequence/BowtieIndex/genome.2.ebwt'
  -      'BDGP6/Sequence/BowtieIndex/genome.3.ebwt' 'BDGP6/Sequence/BowtieIndex/genome.4.ebwt'
  -      'BDGP6/Sequence/BowtieIndex/genome.rev.1.ebwt' 'BDGP6/Sequence/BowtieIndex/genome.rev.2.ebwt';
  -
  -fq-c1-1 = 'fastq/GSM794483_C1_R1_1.fq'
  -          'fastq/GSM794484_C1_R2_1.fq'
  -          'fastq/GSM794485_C1_R3_1.fq';
  -
  -fq-c1-2 = 'fastq/GSM794483_C1_R1_2.fq'
  -          'fastq/GSM794484_C1_R2_2.fq'
  -          'fastq/GSM794485_C1_R3_2.fq';
  -
  -fq-c2-1 = 'fastq/GSM794486_C2_R1_1.fq'
  -          'fastq/GSM794487_C2_R2_1.fq'
  -          'fastq/GSM794488_C2_R3_1.fq';
  -
  -fq-c2-2 = 'fastq/GSM794486_C2_R1_2.fq'
  -          'fastq/GSM794487_C2_R2_2.fq'
  -          'fastq/GSM794488_C2_R3_2.fq';
  +geneanno = "BDGP6/Annotation/Genes/genes.gtf";
  +
  +fa = "BDGP6/Sequence/WholeGenomeFasta/genome.fa";
  +fai = "BDGP6/Sequence/WholeGenomeFasta/genome.fa.fai";
  +
  +idx = "BDGP6/Sequence/BowtieIndex/genome.1.ebwt' 'BDGP6/Sequence/BowtieIndex/genome.2.ebwt"
  +      "BDGP6/Sequence/BowtieIndex/genome.3.ebwt' 'BDGP6/Sequence/BowtieIndex/genome.4.ebwt"
  +      "BDGP6/Sequence/BowtieIndex/genome.rev.1.ebwt' 'BDGP6/Sequence/BowtieIndex/genome.rev.2.ebwt";
  +
  +fq-c1-1 = "fastq/GSM794483_C1_R1_1.fq"
  +          "fastq/GSM794484_C1_R2_1.fq"
  +          "fastq/GSM794485_C1_R3_1.fq";
  +
  +fq-c1-2 = "fastq/GSM794483_C1_R1_2.fq"
  +          "fastq/GSM794484_C1_R2_2.fq"
  +          "fastq/GSM794485_C1_R3_2.fq";
  +
  +fq-c2-1 = "fastq/GSM794486_C2_R1_1.fq"
  +          "fastq/GSM794487_C2_R2_1.fq"
  +          "fastq/GSM794488_C2_R3_1.fq";
  +
  +fq-c2-2 = "fastq/GSM794486_C2_R1_2.fq"
  +          "fastq/GSM794487_C2_R2_2.fq"
  +          "fastq/GSM794488_C2_R3_2.fq";
   
   
   // WORKFLOW
   
   // tophat align
   bam-c1 = tophat-align(
  -             geneanno: geneanno
  -             idx: idx
  -             fa:  fa
  -             fq1: fq-c1-1
  +             geneanno: geneanno,
  +             idx: idx,
  +             fa:  fa,
  +             fq1: fq-c1-1,
                fq2: fq-c1-2 );
           
   bam-c2 = tophat-align(
  -             geneanno: geneanno
  -             idx: idx
  -             fa:  fa
  -             fq1: fq-c2-1
  +             geneanno: geneanno,
  +             idx: idx,
  +             fa:  fa,
  +             fq1: fq-c2-1,
                fq2: fq-c2-2 );
   
   bam = bam-c1 bam-c2;
  
positive.code: transcript-c2 = cufflinks( bam: bam-c2 );
  
  merged = cuffmerge(
    transcript: transcript-c1 transcript-c2
    geneanno: geneanno
    fa: fa
    fai: fai );
  
  diff = cuffdiff(
    merged: merged
    bam1: bam-c1
    bam2: bam-c2
    fa: fa
    fai: fai );
  
  
  
negative.code: 
  // step 14
  bai = samtools-index( bam: bam );
  stats = samtools-idxstats( bam: bam, bai: bai );
  
  // step 15
  comparison = cuffcompare( gtf: transcript-c1 transcript-c2, geneanno: geneanno );
  
  // steps 16 - 18
  diff_genes nsig_gene nsig_isoform nsig_tss nsig_cds nsig_promoter nsig_splicing nsig_relCDS = cummerbund2( diff: diff );
  
  // QUERY
  
  csdensity scatter volcano regucalcin_expression regucalcin_isoforms stats comparison diff_genes nsig_gene nsig_isoform nsig_tss nsig_cds nsig_promoter nsig_splicing nsig_relCDS;
  