cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-caudatum-Hol_S14 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa GSF869-Doak-Ugne-Hol-caudatum_43c3d_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-caudatum-no-Hol_S15 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa GSF869-Doak-Ugne-no-Hol-caudatum_43c3d_annotation_v1.transcriptome.bam