cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-209_S7_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-209_S7_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-Ugne-209_S7-biaurelia_V1-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-209_S7_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-209_S7_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-Ugne-209_S7-caudatum_43c3d_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-209_S7_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-209_S7_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-209_S7-multimicronucleatum_MO3c4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-209_S7_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-209_S7_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-209_S7-primaurelia_Ir4-2_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-209_S7_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-209_S7_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-209_S7-sexaurelia_AZ8-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-209_S7_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-209_S7_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.fa - -o GSF869-Doak-Ugne-209_S7-Paramecium_tetraurelia.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-223_S10_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-223_S10_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-223_S10-biaurelia_V1-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-223_S10_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-223_S10_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-223_S10-caudatum_43c3d_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-223_S10_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-223_S10_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-223_S10-multimicronucleatum_MO3c4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-223_S10_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-223_S10_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-223_S10-primaurelia_Ir4-2_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-223_S10_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-223_S10_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-223_S10-sexaurelia_AZ8-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-223_S10_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-223_S10_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.fa - -o GSF869-Doak-Ugne-223_S10-Paramecium_tetraurelia.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-227_S13_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-227_S13_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-227_S13-biaurelia_V1-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-227_S13_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-227_S13_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-227_S13-caudatum_43c3d_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-227_S13_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-227_S13_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-227_S13-multimicronucleatum_MO3c4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-227_S13_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-227_S13_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-227_S13-primaurelia_Ir4-2_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-227_S13_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-227_S13_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-227_S13-sexaurelia_AZ8-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-227_S13_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-227_S13_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.fa - -o GSF869-Doak-Ugne-227_S13-Paramecium_tetraurelia.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-328_S12_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-328_S12_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-328_S12-biaurelia_V1-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-328_S12_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-328_S12_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-328_S12-caudatum_43c3d_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-328_S12_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-328_S12_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-328_S12-multimicronucleatum_MO3c4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-328_S12_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-328_S12_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-328_S12-primaurelia_Ir4-2_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-328_S12_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-328_S12_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-328_S12-sexaurelia_AZ8-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-328_S12_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-328_S12_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.fa - -o GSF869-Doak-Ugne-328_S12-Paramecium_tetraurelia.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-NiA_S11_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-NiA_S11_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-NiA_S11-biaurelia_V1-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-NiA_S11_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-NiA_S11_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-NiA_S11-caudatum_43c3d_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-NiA_S11_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-NiA_S11_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-NiA_S11-multimicronucleatum_MO3c4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-NiA_S11_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-NiA_S11_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-NiA_S11-primaurelia_Ir4-2_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-NiA_S11_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-NiA_S11_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-NiA_S11-sexaurelia_AZ8-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-NiA_S11_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-NiA_S11_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.fa - -o GSF869-Doak-Ugne-NiA_S11-Paramecium_tetraurelia.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-V1-4_S9_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-V1-4_S9_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-V1-4_S9-biaurelia_V1-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-V1-4_S9_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-V1-4_S9_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-V1-4_S9-caudatum_43c3d_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-V1-4_S9_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-V1-4_S9_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-V1-4_S9-multimicronucleatum_MO3c4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-V1-4_S9_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-V1-4_S9_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-V1-4_S9-primaurelia_Ir4-2_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-V1-4_S9_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-V1-4_S9_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_annotation_v1.transcriptome.fa - -o GSF869-Doak-Ugne-V1-4_S9-sexaurelia_AZ8-4_annotation_v1.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-V1-4_S9_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-V1-4_S9_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20.transcriptome.fa - -o GSF869-Doak-Ugne-V1-4_S9-Paramecium_tetraurelia.transcriptome.bam