cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-para2_1_sequence.txt.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-strain_V1-4-autogamy-110506_IRIS_00020-para2_1_sequence.txt.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-141105-bi_CCGTCCCG_L001_R1_001.fastq.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-strain_V1-4-autogamy-141105-bi_CCGTCCCG_L001_R1_001.fastq.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1_1_sequence.txt.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-strain_V1-4-vegetative-110506_IRIS_00020-para1_1_sequence.txt.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-141105-2V_AGTCAACA_L001_R1_00.fastq.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-strain_V1-4-vegetative-141105-2V_AGTCAACA_L001_R1_00.fastq.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-strain_43c3d-vegetative-CNNNCC_S8_L001_R1_001.1x100mers.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-strain_43c3d-vegetative-CNNNCC_S8_L001_R1_001.1x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-strain_43c3d-vegetative-raw_reads-Lynch508-_S1_L001_R1_001.fastq.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-strain_43c3d-vegetative-raw_reads-Lynch508-_S1_L001_R1_001.fastq.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-strain_43c3d-vegetative-raw_reads-Lynch508D-Paramecium_S8_L001_R1_001.fastq.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-strain_43c3d-vegetative-raw_reads-Lynch508D-Paramecium_S8_L001_R1_001.fastq.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-strain_CA1-autogamy-141105-sex_GTGAAACG_L001_R1_001.fastq.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-strain_CA1-autogamy-141105-sex_GTGAAACG_L001_R1_001.fastq.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3_1_sequence.txt.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-strain_CA1-vegetative-110506_IRIS_00020-para3_1_sequence.txt.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-141105-6V_ATGTCAGA_L001_R1_001.fastq.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-strain_CA1-vegetative-141105-6V_ATGTCAGA_L001_R1_001.fastq.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-tetraurelia-strain_unknown_1-autogamy-141105-tet_GTCCGCAC_L001_R1_001.fastq.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-tetraurelia-strain_unknown_1-autogamy-141105-tet_GTCCGCAC_L001_R1_001.fastq.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4_1_sequence.txt.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-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4_1_sequence.txt.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-141105-4V_AGTTCCGT_L001_R1_00.fastq.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-tetraurelia-strain_unknown_1-vegetative-141105-4V_AGTTCCGT_L001_R1_00.fastq.2x100mers.InsLength &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-para2_1_sequence.txt.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-strain_V1-4-autogamy-110506_IRIS_00020-para2_1_sequence.txt.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-strain_V1-4-autogamy-141105-bi_CCGTCCCG_L001_R1_001.fastq.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-strain_V1-4-autogamy-141105-bi_CCGTCCCG_L001_R1_001.fastq.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1_1_sequence.txt.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-strain_V1-4-vegetative-110506_IRIS_00020-para1_1_sequence.txt.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-biaurelia-strain_V1-4-vegetative-141105-2V_AGTCAACA_L001_R1_00.fastq.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-strain_V1-4-vegetative-141105-2V_AGTCAACA_L001_R1_00.fastq.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-strain_43c3d-vegetative-CNNNCC_S8_L001_R1_001.1x100mers.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-strain_43c3d-vegetative-CNNNCC_S8_L001_R1_001.1x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-strain_43c3d-vegetative-raw_reads-Lynch508-_S1_L001_R1_001.fastq.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-strain_43c3d-vegetative-raw_reads-Lynch508-_S1_L001_R1_001.fastq.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-caudatum-strain_43c3d-vegetative-raw_reads-Lynch508D-Paramecium_S8_L001_R1_001.fastq.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-strain_43c3d-vegetative-raw_reads-Lynch508D-Paramecium_S8_L001_R1_001.fastq.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-strain_CA1-autogamy-141105-sex_GTGAAACG_L001_R1_001.fastq.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-strain_CA1-autogamy-141105-sex_GTGAAACG_L001_R1_001.fastq.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3_1_sequence.txt.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-strain_CA1-vegetative-110506_IRIS_00020-para3_1_sequence.txt.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-sexaurelia-strain_CA1-vegetative-141105-6V_ATGTCAGA_L001_R1_001.fastq.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-strain_CA1-vegetative-141105-6V_ATGTCAGA_L001_R1_001.fastq.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-tetraurelia-strain_unknown_1-autogamy-141105-tet_GTCCGCAC_L001_R1_001.fastq.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-tetraurelia-strain_unknown_1-autogamy-141105-tet_GTCCGCAC_L001_R1_001.fastq.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4_1_sequence.txt.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-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4_1_sequence.txt.2x100mers.unique.InsLength -nomulti &
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEInsertDistFromBAM.py Paramecium-tetraurelia-strain_unknown_1-vegetative-141105-4V_AGTTCCGT_L001_R1_00.fastq.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-tetraurelia-strain_unknown_1-vegetative-141105-4V_AGTTCCGT_L001_R1_00.fastq.2x100mers.unique.InsLength -nomulti &