cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_2V.end1.100mers.fastq.bz2 Sample_2V.end2.100mers.fastq.bz2 | /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 Paramecium-biaurelia-Sample_2V.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_bi.end1.100mers.fastq.bz2 Sample_bi.end2.100mers.fastq.bz2 | /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 Paramecium-biaurelia-Sample_bi.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_2D1.end1.100mers.fastq.bz2 Sample_2D1.end2.100mers.fastq.bz2 | /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 Paramecium-biaurelia-Sample_2D1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_2D2.end1.100mers.fastq.bz2 Sample_2D2.end2.100mers.fastq.bz2 | /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 Paramecium-biaurelia-Sample_2D2.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_c3d_1.end1.100mers.fastq.bz2 Sample_c3d_1.end2.100mers.fastq.bz2 | /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 --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 Paramecium-caudatum-Sample_c3d_1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_c3d_2.end1.100mers.fastq.bz2 Sample_c3d_2.end2.100mers.fastq.bz2 | /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 --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 Paramecium-caudatum-Sample_c3d_2.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_MPF1.end1.100mers.fastq.bz2 Sample_MPF1.end2.100mers.fastq.bz2 | /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 --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 Paramecium-caudatum-Sample_MPF1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_1V.end1.100mers.fastq.bz2 Sample_1V.end2.100mers.fastq.bz2 | /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 Paramecium-primaurelia-Sample_1V.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_1D1.end1.100mers.fastq.bz2 Sample_1D1.end2.100mers.fastq.bz2 | /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 Paramecium-primaurelia-Sample_1D1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_1D2.end1.100mers.fastq.bz2 Sample_1D2.end2.100mers.fastq.bz2 | /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 Paramecium-primaurelia-Sample_1D2.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_6D1.end1.100mers.fastq.bz2 Sample_6D1.end2.100mers.fastq.bz2 | /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 Paramecium-sexaurelia-Sample_6D1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_6D2.end1.100mers.fastq.bz2 Sample_6D2.end2.100mers.fastq.bz2 | /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 Paramecium-sexaurelia-Sample_6D2.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_6V.end1.100mers.fastq.bz2 Sample_6V.end2.100mers.fastq.bz2 | /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 Paramecium-sexaurelia-Sample_6V.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_4D_2_14_16_12.end1.100mers.fastq.bz2 Sample_4D_2_14_16_12.end2.100mers.fastq.bz2 | /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 Paramecium-teraurelia-Sample_4D_2_14_16_12.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_4D1.end1.100mers.fastq.bz2 Sample_4D1.end2.100mers.fastq.bz2 | /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 Paramecium-teraurelia-Sample_4D1.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_4D2.end1.100mers.fastq.bz2 Sample_4D2.end2.100mers.fastq.bz2 | /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 Paramecium-teraurelia-Sample_4D2.2x100mers.a.e200.offrate1.bam
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Sample_172.end1.100mers.fastq.bz2 Sample_172.end2.100mers.fastq.bz2 | /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 Paramecium-teraurelia-Sample_172.2x100mers.a.e200.offrate1.bam