cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --output-dir Paramecium-caudatum-Hol_S14-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-caudatum_43c3d_annotation_v1 Paramecium-caudatum-Hol_S14-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --compatible-hits-norm --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --output-dir Paramecium-caudatum-no-Hol_S15-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-caudatum_43c3d_annotation_v1 Paramecium-caudatum-no-Hol_S15-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium-biaurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium-biaurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium-biaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-biaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium_primaurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_primaurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium_primaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_primaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium_primaurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_primaurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium_primaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_primaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium-sexaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-sexaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium-sexaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium-sexaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium_tetraurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium_tetraurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium_tetraurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium_tetraurelia-GSF869-Doak-Ugne-328_S12-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-GSF869-Doak-Ugne-328_S12-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -p 16 --output-dir Paramecium_tetraurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tetraurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Paramecium-biaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-primaurelia_Ir4-2_annotation_v1 Paramecium_primaurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-primaurelia_Ir4-2_annotation_v1 Paramecium_primaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-primaurelia_Ir4-2_annotation_v1 Paramecium_primaurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-primaurelia_Ir4-2_annotation_v1 Paramecium_primaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-sexaurelia_AZ8-4_annotation_v1 Paramecium-sexaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-sexaurelia_AZ8-4_annotation_v1 Paramecium-sexaurelia-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-328_S12-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-GSF869-Doak-Ugne-328_S12-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks --min-intron-length 10 -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-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-Paramecium_tetraurelia.GCA_000165425 Paramecium_tetraurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam