cd /N/dc2/projects/marinovg/Paramecium/variation/2016-04-04-LAST; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /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_assembly_v1+chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort - Sample_16I-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/Paramecium/variation/2016-04-04-LAST; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /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_assembly_v1+chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort - Sample_C026-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/Paramecium/variation/2016-04-04-LAST; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Canal-1I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /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_assembly_v1 -p 8 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_Canal-1I-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/Paramecium/variation/2016-04-04-LAST; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /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_assembly_v1 -p 8 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_M08-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/Paramecium/variation/2016-04-04-LAST; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /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_assembly_v1 -p 8 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_M13-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/Paramecium/variation/2016-04-04-LAST; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /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_assembly_v1 -p 8 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_M15-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/Paramecium/variation/2016-04-04-LAST; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /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_assembly_v1 -p 8 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_Peniche3I-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/Paramecium/variation/2016-04-04-LAST; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_TRB101-4/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /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_assembly_v1 -p 8 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bowtie-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_TRB101-4-reads.end1.multimicronucleatum.unique