cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 30000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.30M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 30000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.30M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 30000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - -o Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.30M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 30000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.fa - -o Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.30M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 25000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.25M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 25000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.25M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 25000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - -o Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.25M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 25000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.fa - -o Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.25M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 20000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.20M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 20000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.20M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 20000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - -o Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.20M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 20000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.fa - -o Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.20M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 15000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.15M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 15000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.15M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 15000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - -o Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.15M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 15000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.fa - -o Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.15M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 10000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.10M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 10000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.10M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 10000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - -o Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.10M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 10000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.fa - -o Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.10M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 5000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.5M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 5000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.5M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 5000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - -o Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.5M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 5000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.fa - -o Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.5M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 2000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.2M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 2000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.2M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 2000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - -o Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.2M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 2000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.fa - -o Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.2M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 1000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.1M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 1000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.1M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 1000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - -o Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.1M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 1000000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.fa - -o Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.1M.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 500000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10.500K.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 500000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - -o Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10.500K.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 500000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - -o Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10.500K.bam &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/sampleBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10/accepted_hits.bam samtools 500000 | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.fa - -o Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10.500K.bam &