anchor.diff:  transcript-c2 = cufflinks( bam: bam-c2 );
   
   merged = cuffmerge(
  -  transcript: transcript-c1 transcript-c2
  -  geneanno: geneanno
  -  fa: fa
  +  transcript: transcript-c1 transcript-c2,
  +  geneanno: geneanno,
  +  fa: fa,
     fai: fai );
   
   diff = cuffdiff(
  -  merged: merged
  -  bam1: bam-c1
  -  bam2: bam-c2
  -  fa: fa
  +  merged: merged,
  +  bam1: bam-c1,
  +  bam2: bam-c2,
  +  fa: fa,
     fai: fai );
   
   
  
positive.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;
negative.code: 
  // 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";
  
  
  // WORKFLOW
  
  // tophat align
  bam-c1 = tophat-align(
               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,
               fq2: fq-c2-2 );
  
  bam = bam-c1 bam-c2;
  