cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-biaurelia-Sample_2V-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-Sample_2V-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-biaurelia-Sample_bi-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-Sample_bi-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-biaurelia-Sample_2D1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-Sample_2D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-biaurelia-Sample_2D2-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-Sample_2D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_primaurelia-Sample_1V-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_primaurelia-Sample_1V-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_primaurelia-Sample_1D1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_primaurelia-Sample_1D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_primaurelia-Sample_1D2-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_primaurelia-Sample_1D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-sexaurelia-Sample_6D1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-sexaurelia-Sample_6D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-sexaurelia-Sample_6D2-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-sexaurelia-Sample_6D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-sexaurelia-Sample_6V-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-sexaurelia-Sample_6V-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_tetraurelia-Sample_4D1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-Sample_4D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_tetraurelia-Sample_4D2-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-Sample_4D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_tetraurelia-Sample_172-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-Sample_172-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --output-dir Paramecium-biaurelia-Sample_2V-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-Sample_2V-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --output-dir Paramecium-biaurelia-Sample_bi-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-Sample_bi-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --output-dir Paramecium-biaurelia-Sample_2D1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-Sample_2D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --output-dir Paramecium-biaurelia-Sample_2D2-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-Sample_2D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --output-dir Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-caudatum_43c3d_annotation_v1 Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --output-dir Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-caudatum_43c3d_annotation_v1 Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --output-dir Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-caudatum_43c3d_annotation_v1 Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --output-dir Paramecium_primaurelia-Sample_1V-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-primaurelia_Ir4-2_annotation_v1 Paramecium_primaurelia-Sample_1V-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --output-dir Paramecium_primaurelia-Sample_1D1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-primaurelia_Ir4-2_annotation_v1 Paramecium_primaurelia-Sample_1D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --output-dir Paramecium_primaurelia-Sample_1D2-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-primaurelia_Ir4-2_annotation_v1 Paramecium_primaurelia-Sample_1D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --output-dir Paramecium-sexaurelia-Sample_6D1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-sexaurelia_AZ8-4_annotation_v1 Paramecium-sexaurelia-Sample_6D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --output-dir Paramecium-sexaurelia-Sample_6D2-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-sexaurelia_AZ8-4_annotation_v1 Paramecium-sexaurelia-Sample_6D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --output-dir Paramecium-sexaurelia-Sample_6V-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-sexaurelia_AZ8-4_annotation_v1 Paramecium-sexaurelia-Sample_6V-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --output-dir Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --output-dir Paramecium_tetraurelia-Sample_4D1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-Sample_4D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --output-dir Paramecium_tetraurelia-Sample_4D2-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-Sample_4D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --output-dir Paramecium_tetraurelia-Sample_172-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-Sample_172-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-biaurelia-Sample_2V-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-Sample_2V-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-biaurelia-Sample_bi-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-Sample_bi-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-biaurelia-Sample_2D1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-Sample_2D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-biaurelia-Sample_2D2-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-Sample_2D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_primaurelia-Sample_1V-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_primaurelia-Sample_1V-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_primaurelia-Sample_1D1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_primaurelia-Sample_1D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_primaurelia-Sample_1D2-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_primaurelia-Sample_1D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-sexaurelia-Sample_6D1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-sexaurelia-Sample_6D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-sexaurelia-Sample_6D2-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-sexaurelia-Sample_6D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium-sexaurelia-Sample_6V-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-sexaurelia-Sample_6V-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_tetraurelia-Sample_4D1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-Sample_4D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_tetraurelia-Sample_4D2-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-Sample_4D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_tetraurelia-Sample_172-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-Sample_172-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --output-dir Paramecium-biaurelia-Sample_2V-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-Sample_2V-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --output-dir Paramecium-biaurelia-Sample_bi-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-Sample_bi-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --output-dir Paramecium-biaurelia-Sample_2D1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-Sample_2D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --output-dir Paramecium-biaurelia-Sample_2D2-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-Sample_2D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --output-dir Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-caudatum_43c3d_annotation_v1 Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --output-dir Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-caudatum_43c3d_annotation_v1 Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --output-dir Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-caudatum_43c3d_annotation_v1 Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --output-dir Paramecium_primaurelia-Sample_1V-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-primaurelia_Ir4-2_annotation_v1 Paramecium_primaurelia-Sample_1V-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --output-dir Paramecium_primaurelia-Sample_1D1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-primaurelia_Ir4-2_annotation_v1 Paramecium_primaurelia-Sample_1D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --output-dir Paramecium_primaurelia-Sample_1D2-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-primaurelia_Ir4-2_annotation_v1 Paramecium_primaurelia-Sample_1D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --output-dir Paramecium-sexaurelia-Sample_6D1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-sexaurelia_AZ8-4_annotation_v1 Paramecium-sexaurelia-Sample_6D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --output-dir Paramecium-sexaurelia-Sample_6D2-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-sexaurelia_AZ8-4_annotation_v1 Paramecium-sexaurelia-Sample_6D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --output-dir Paramecium-sexaurelia-Sample_6V-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-sexaurelia_AZ8-4_annotation_v1 Paramecium-sexaurelia-Sample_6V-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --output-dir Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --output-dir Paramecium_tetraurelia-Sample_4D1-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-Sample_4D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --output-dir Paramecium_tetraurelia-Sample_4D2-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-Sample_4D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --output-dir Paramecium_tetraurelia-Sample_172-2x150-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-Sample_172-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam