cd /N/dc2/projects/marinovg/2015-04-23-Paramecium-stringtie; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_octaurelia_K8_CA1-Sample_8V-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_octaurelia_K8_CA1-Sample_8V-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-04-23-Paramecium-stringtie; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_octaurelia_K8_CA1-Sample_8D1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_octaurelia_K8_CA1-Sample_8D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam 
cd /N/dc2/projects/marinovg/2015-04-23-Paramecium-stringtie; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_tredecaurelia_209_CA2-Sample_209_13-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_tredecaurelia_209_CA2-Sample_209_13-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/2015-04-23-Paramecium-stringtie; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Paramecium_octaurelia_K8_CA1-Sample_8V+8D1-2x100-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Paramecium_octaurelia_K8_CA1-Sample_8V+8D1-2x100-TopHat-2.0.8-minIntron10.sorted.bam