export PATH=/N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/:$PATH; cd /N/dc2/projects/marinovg/2015-05-27-UTRs; /N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/cuffmerge -p 16 -o cuffmerge-2.2.0-Paramecium_biaurelia --ref-gtf /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium_biaurelia.assembly_list.txt
export PATH=/N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/:$PATH; cd /N/dc2/projects/marinovg/2015-05-27-UTRs; /N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/cuffmerge -p 16 -o cuffmerge-2.2.0-Paramecium_caudatum --ref-gtf /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf Paramecium_caudatum.assembly_list.txt
export PATH=/N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/:$PATH; cd /N/dc2/projects/marinovg/2015-05-27-UTRs; /N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/cuffmerge -p 16 -o cuffmerge-2.2.0-Paramecium_primaurelia --ref-gtf /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia.assembly_list.txt
export PATH=/N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/:$PATH; cd /N/dc2/projects/marinovg/2015-05-27-UTRs; /N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/cuffmerge -p 16 -o cuffmerge-2.2.0-Paramecium_sexaurelia --ref-gtf /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf Paramecium_sexaurelia.assembly_list.txt
export PATH=/N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/:$PATH; cd /N/dc2/projects/marinovg/2015-05-27-UTRs; /N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/cuffmerge -p 16 -o cuffmerge-2.2.0-Paramecium_tetraurelia --ref-gtf /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia.assembly_list.txt