cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-biaurelia-Sample_2V /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.fa Paramecium-biaurelia-Sample_2V.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-biaurelia-Sample_bi /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.fa Paramecium-biaurelia-Sample_bi.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-biaurelia-Sample_2D1 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.fa Paramecium-biaurelia-Sample_2D1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-biaurelia-Sample_2D2 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.fa Paramecium-biaurelia-Sample_2D2.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-caudatum-Sample_c3d_1 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa Paramecium-caudatum-Sample_c3d_1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-caudatum-Sample_c3d_2 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa Paramecium-caudatum-Sample_c3d_2.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-caudatum-Sample_MPF1 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa Paramecium-caudatum-Sample_MPF1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-primaurelia-Sample_1V /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.fa Paramecium-primaurelia-Sample_1V.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-primaurelia-Sample_1D1 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.fa Paramecium-primaurelia-Sample_1D1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-primaurelia-Sample_1D2 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.fa Paramecium-primaurelia-Sample_1D2.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-sexaurelia-Sample_6D1 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.fa Paramecium-sexaurelia-Sample_6D1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-sexaurelia-Sample_6D2 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.fa Paramecium-sexaurelia-Sample_6D2.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-sexaurelia-Sample_6V /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.fa Paramecium-sexaurelia-Sample_6V.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-tetraurelia-Sample_4D_2_14_16_12 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.fa Paramecium-teraurelia-Sample_4D_2_14_16_12.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-tetraurelia-Sample_4D1 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.fa Paramecium-teraurelia-Sample_4D1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-tetraurelia-Sample_4D2 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.fa Paramecium-teraurelia-Sample_4D2.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; /N/dc2/projects/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-rf-2x100mers-Paramecium-tetraurelia-Sample_172 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.fa Paramecium-teraurelia-Sample_172.2x100mers.a.e200.offrate1.bam