cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-Sample_2V-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-Sample_2V-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-Sample_bi-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-Sample_bi-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-Sample_2D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-Sample_2D1-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-Sample_2D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-Sample_2D2-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia-Sample_1V-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes sam_reads_genes-Paramecium_primaurelia-Sample_1V-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia-Sample_1D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes sam_reads_genes-Paramecium_primaurelia-Sample_1D1-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia-Sample_1D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes sam_reads_genes-Paramecium_primaurelia-Sample_1D2-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf Paramecium-sexaurelia-Sample_6D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-sexaurelia-Sample_6D1-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf Paramecium-sexaurelia-Sample_6D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-sexaurelia-Sample_6D2-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf Paramecium-sexaurelia-Sample_6V-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-sexaurelia-Sample_6V-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-Sample_4D1-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-Sample_4D1-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-Sample_4D2-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-Sample_4D2-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-Sample_172-2x150-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-Sample_172-2x150 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-Sample_2V-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-Sample_2V-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-Sample_bi-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-Sample_bi-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-Sample_2D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-Sample_2D1-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium-biaurelia-Sample_2D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-biaurelia-Sample_2D2-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia-Sample_1V-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes sam_reads_genes-Paramecium_primaurelia-Sample_1V-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia-Sample_1D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes sam_reads_genes-Paramecium_primaurelia-Sample_1D1-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia-Sample_1D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_assembly_v1.chrom.sizes sam_reads_genes-Paramecium_primaurelia-Sample_1D2-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf Paramecium-sexaurelia-Sample_6D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-sexaurelia-Sample_6D1-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf Paramecium-sexaurelia-Sample_6D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-sexaurelia-Sample_6D2-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf Paramecium-sexaurelia-Sample_6V-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_assembly_v1.chrom.sizes sam_reads_genes-Paramecium-sexaurelia-Sample_6V-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-Sample_4D1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-Sample_4D1-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-Sample_4D2-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-Sample_4D2-2x100 -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf Paramecium_tetraurelia-Sample_172-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.chrom.sizes sam_reads_genes-Paramecium_tetraurelia-Sample_172-2x100 -nomulti