cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-NiA_S11-Paramecium_tetraurelia.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes GSF869-Doak-Ugne-NiA_S11-Paramecium_tetraurelia.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-209_S7-Paramecium_tetraurelia.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes GSF869-Doak-Ugne-209_S7-Paramecium_tetraurelia.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-223_S10-Paramecium_tetraurelia.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes GSF869-Doak-Ugne-223_S10-Paramecium_tetraurelia.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-V1-4_S9-Paramecium_tetraurelia.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes GSF869-Doak-Ugne-V1-4_S9-Paramecium_tetraurelia.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-227_S13-Paramecium_tetraurelia.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes GSF869-Doak-Ugne-227_S13-Paramecium_tetraurelia.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-328_S12-Paramecium_tetraurelia.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes GSF869-Doak-Ugne-328_S12-Paramecium_tetraurelia.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-209_S7-multimicronucleatum_MO3c4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-209_S7-multimicronucleatum_MO3c4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-223_S10-multimicronucleatum_MO3c4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-223_S10-multimicronucleatum_MO3c4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-NiA_S11-multimicronucleatum_MO3c4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-NiA_S11-multimicronucleatum_MO3c4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-227_S13-multimicronucleatum_MO3c4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-227_S13-multimicronucleatum_MO3c4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-328_S12-multimicronucleatum_MO3c4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-328_S12-multimicronucleatum_MO3c4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-V1-4_S9-multimicronucleatum_MO3c4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-V1-4_S9-multimicronucleatum_MO3c4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-209_S7-primaurelia_Ir4-2_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-209_S7-primaurelia_Ir4-2_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-223_S10-primaurelia_Ir4-2_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-223_S10-primaurelia_Ir4-2_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-328_S12-primaurelia_Ir4-2_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-328_S12-primaurelia_Ir4-2_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-227_S13-primaurelia_Ir4-2_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-227_S13-primaurelia_Ir4-2_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-NiA_S11-primaurelia_Ir4-2_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-NiA_S11-primaurelia_Ir4-2_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-V1-4_S9-primaurelia_Ir4-2_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-V1-4_S9-primaurelia_Ir4-2_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-209_S7-sexaurelia_AZ8-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-209_S7-sexaurelia_AZ8-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-223_S10-sexaurelia_AZ8-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-223_S10-sexaurelia_AZ8-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-227_S13-sexaurelia_AZ8-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-227_S13-sexaurelia_AZ8-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-328_S12-sexaurelia_AZ8-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-328_S12-sexaurelia_AZ8-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-NiA_S11-sexaurelia_AZ8-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-NiA_S11-sexaurelia_AZ8-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-V1-4_S9-sexaurelia_AZ8-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-V1-4_S9-sexaurelia_AZ8-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-223_S10-biaurelia_V1-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-223_S10-biaurelia_V1-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-227_S13-biaurelia_V1-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-227_S13-biaurelia_V1-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-Ugne-209_S7-biaurelia_V1-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-Ugne-209_S7-biaurelia_V1-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-V1-4_S9-biaurelia_V1-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-V1-4_S9-biaurelia_V1-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-328_S12-biaurelia_V1-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-328_S12-biaurelia_V1-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-NiA_S11-biaurelia_V1-4_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-NiA_S11-biaurelia_V1-4_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-no-Hol-caudatum_43c3d_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-no-Hol-caudatum_43c3d_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-Hol-caudatum_43c3d_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-Hol-caudatum_43c3d_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-223_S10-caudatum_43c3d_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-223_S10-caudatum_43c3d_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-V1-4_S9-caudatum_43c3d_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-V1-4_S9-caudatum_43c3d_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-Ugne-209_S7-caudatum_43c3d_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-Ugne-209_S7-caudatum_43c3d_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-328_S12-caudatum_43c3d_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-328_S12-caudatum_43c3d_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-227_S13-caudatum_43c3d_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-227_S13-caudatum_43c3d_annotation_v1.transcriptome.InsLen &
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py GSF869-Doak-Ugne-NiA_S11-caudatum_43c3d_annotation_v1.transcriptome.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes GSF869-Doak-Ugne-NiA_S11-caudatum_43c3d_annotation_v1.transcriptome.InsLen &