cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_16I-reads.end1.biaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_C026-reads.end1.biaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_Canal-1I-reads.end1.biaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M08-reads.end1.biaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M13-reads.end1.biaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M15-reads.end1.biaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_Peniche3I-reads.end1.biaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bwa-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_TRB101-4-reads.end1.biaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort - Sample_16I-reads.end1.caudatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort - Sample_C026-reads.end1.caudatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort - Sample_Canal-1I-reads.end1.caudatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort - Sample_M08-reads.end1.caudatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort - Sample_M13-reads.end1.caudatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort - Sample_M15-reads.end1.caudatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort - Sample_Peniche3I-reads.end1.caudatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bwa-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort - Sample_TRB101-4-reads.end1.caudatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_16I-reads.end1.multimicronucleatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_C026-reads.end1.multimicronucleatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_Canal-1I-reads.end1.multimicronucleatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_M08-reads.end1.multimicronucleatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_M13-reads.end1.multimicronucleatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_M15-reads.end1.multimicronucleatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_Peniche3I-reads.end1.multimicronucleatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_multimicronucleatum_MO3c4/bwa-indexes/multimicronucleatum_MO3c4_assembly_v1.fa - | samtools sort - Sample_TRB101-4-reads.end1.multimicronucleatum.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_16I-reads.end1.octaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_C026-reads.end1.octaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_Canal-1I-reads.end1.octaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M08-reads.end1.octaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M13-reads.end1.octaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M15-reads.end1.octaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_Peniche3I-reads.end1.octaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bwa-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_TRB101-4-reads.end1.octaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_16I-reads.end1.pentaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_C026-reads.end1.pentaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_Canal-1I-reads.end1.pentaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M08-reads.end1.pentaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M13-reads.end1.pentaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M15-reads.end1.pentaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_Peniche3I-reads.end1.pentaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_pentaurelia_87E+87O/bwa-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_TRB101-4-reads.end1.pentaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_16I-reads.end1.primaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_C026-reads.end1.primaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_Canal-1I-reads.end1.primaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M08-reads.end1.primaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M13-reads.end1.primaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M15-reads.end1.primaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_Peniche3I-reads.end1.primaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bwa-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_TRB101-4-reads.end1.primaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_16I-reads.end1.sexaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_C026-reads.end1.sexaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_Canal-1I-reads.end1.sexaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M08-reads.end1.sexaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M13-reads.end1.sexaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M15-reads.end1.sexaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_Peniche3I-reads.end1.sexaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bwa-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_TRB101-4-reads.end1.sexaurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_16I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_16I-reads.end1.tetraurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C026/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_C026-reads.end1.tetraurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_Canal-1I-reads.end1.tetraurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M08/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M08-reads.end1.tetraurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M13/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M13-reads.end1.tetraurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M15/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M15-reads.end1.tetraurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa '<zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Peniche3I/reads.end1.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_Peniche3I-reads.end1.tetraurelia.50mers-20-70.unique.bwa
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; /N/dc2/projects/marinovg/programs/bwa-0.7.12/bwa mem -t 16 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa '<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 -trim5 20' | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bwa-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_TRB101-4-reads.end1.tetraurelia.50mers-20-70.unique.bwa