cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Conjugation-2h-GSM692085-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Conjugation-2h-GSM692085-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Conjugation-8h-GSM692086-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Conjugation-8h-GSM692086-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Growth-m-GSM692081-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Growth-m-GSM692081-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Starvation-15h-VI-GSM692084-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Starvation-15h-VI-GSM692084-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Starvation-3h-V-GSM692083-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Starvation-3h-V-GSM692083-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /N/dc2/projects/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 16 --output-dir Starvation-3h-VI-GSM692082-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-de-novo Starvation-3h-VI-GSM692082-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /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/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf --output-dir Conjugation-2h-GSM692085-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Conjugation-2h-GSM692085-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /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/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf --output-dir Conjugation-8h-GSM692086-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Conjugation-8h-GSM692086-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /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/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf --output-dir Growth-m-GSM692081-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Growth-m-GSM692081-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /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/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf --output-dir Starvation-15h-VI-GSM692084-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-biaurelia_V1-4_annotation_v1 Starvation-15h-VI-GSM692084-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /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/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf --output-dir Starvation-3h-V-GSM692083-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-caudatum_43c3d_annotation_v1 Starvation-3h-V-GSM692083-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; /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/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf --output-dir Starvation-3h-VI-GSM692082-2x75-TopHat-2.0.8-minIntron10/Cufflinks-2.0.2-caudatum_43c3d_annotation_v1 Starvation-3h-VI-GSM692082-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam