cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100.30M Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.30M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100.30M Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.30M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100.30M Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.30M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100.30M Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.30M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100.25M Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.25M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100.25M Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.25M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100.25M Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.25M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100.25M Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.25M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100.20M Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.20M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100.20M Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.20M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100.20M Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.20M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100.20M Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.20M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100.15M Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.15M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100.15M Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.15M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100.15M Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.15M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100.15M Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.15M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100.10M Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.10M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100.10M Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.10M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100.10M Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.10M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100.10M Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.10M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100.5M Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.5M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100.5M Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.5M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100.5M Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.5M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100.5M Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.5M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100.2M Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.2M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100.2M Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.2M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100.2M Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.2M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100.2M Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.2M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100.1M Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.1M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100.1M Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.1M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100.1M Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.1M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100.1M Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.1M.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100.500K Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.500K.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100.500K Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.500K.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100.500K Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.500K.bam
cd /N/dc2/projects/marinovg/2015-02-13-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 Cufflinks-2.0.2-Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100.500K Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.500K.bam