cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-Sample_2V.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes Paramecium-biaurelia-Sample_2V.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-Sample_bi.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes Paramecium-biaurelia-Sample_bi.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-Sample_2D1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes Paramecium-biaurelia-Sample_2D1.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-Sample_2D2.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes Paramecium-biaurelia-Sample_2D2.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-Sample_c3d_1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes Paramecium-caudatum-Sample_c3d_1.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-Sample_c3d_2.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes Paramecium-caudatum-Sample_c3d_2.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-Sample_MPF1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes Paramecium-caudatum-Sample_MPF1.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-primaurelia-Sample_1V.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-primaurelia-Sample_1V.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-primaurelia-Sample_1D1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-primaurelia-Sample_1D1.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-primaurelia-Sample_1D2.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-primaurelia-Sample_1D2.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-Sample_6D1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-sexaurelia-Sample_6D1.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-Sample_6D2.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-sexaurelia-Sample_6D2.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-Sample_6V.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-sexaurelia-Sample_6V.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-teraurelia-Sample_4D_2_14_16_12.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes Paramecium-teraurelia-Sample_4D_2_14_16_12.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-teraurelia-Sample_4D1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes Paramecium-teraurelia-Sample_4D1.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-teraurelia-Sample_4D2.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes Paramecium-teraurelia-Sample_4D2.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-teraurelia-Sample_172.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes Paramecium-teraurelia-Sample_172.2x100mers.InsLength
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-Sample_2V.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes Paramecium-biaurelia-Sample_2V.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-Sample_bi.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes Paramecium-biaurelia-Sample_bi.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-Sample_2D1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes Paramecium-biaurelia-Sample_2D1.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-Sample_2D2.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.chrom.sizes Paramecium-biaurelia-Sample_2D2.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-Sample_c3d_1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes Paramecium-caudatum-Sample_c3d_1.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-Sample_c3d_2.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes Paramecium-caudatum-Sample_c3d_2.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-Sample_MPF1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.chrom.sizes Paramecium-caudatum-Sample_MPF1.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-primaurelia-Sample_1V.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-primaurelia-Sample_1V.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-primaurelia-Sample_1D1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-primaurelia-Sample_1D1.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-primaurelia-Sample_1D2.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-primaurelia-Sample_1D2.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-Sample_6D1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-sexaurelia-Sample_6D1.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-Sample_6D2.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-sexaurelia-Sample_6D2.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-Sample_6V.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.chrom.sizes Paramecium-sexaurelia-Sample_6V.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-teraurelia-Sample_4D_2_14_16_12.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes Paramecium-teraurelia-Sample_4D_2_14_16_12.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-teraurelia-Sample_4D1.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes Paramecium-teraurelia-Sample_4D1.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-teraurelia-Sample_4D2.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes Paramecium-teraurelia-Sample_4D2.2x100mers.unique.InsLength -nomulti
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-teraurelia-Sample_172.2x100mers.a.e200.offrate1.sorted.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.chrom.sizes Paramecium-teraurelia-Sample_172.2x100mers.unique.InsLength -nomulti