cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_1038/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_1038-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_116/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_116-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_126/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_126-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_127/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_127-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_128/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_128-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_129/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_129-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_130/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_130-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_131/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_131-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_132/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_132-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_133/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_133-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_134/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_134-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_137/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_137-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_169/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_169-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_16I-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_256-UB2/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_256-UB2-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_258-UB4/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_258-UB4-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_265/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_265-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_291/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_291-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_298/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_298-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_31/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_31-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_379/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_379-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_44/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_44-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_45/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_45-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_47/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_47-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_51/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_51-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_562alpha/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_562alpha-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_76/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_76-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_7K/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_7K-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_98/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_98-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_99/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_99-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_A-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A30/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_A30-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_B/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_B-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C023/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_C023-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_C026-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C033/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_C033-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C065/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_C065-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C083/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_C083-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C104/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_C104-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C119/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_C119-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C131/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_C131-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C147/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_C147-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_Canal-1I-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Indo1-7I/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_Indo1-7I-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M02/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M02-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M03/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M03-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M04/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M04-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M05/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M05-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M08-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M09/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M09-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M12/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M12-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M13-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_M15-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Moz13BIII/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_Moz13BIII-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_Peniche3I-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_TRB101-4-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_USBL-36I1/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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_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_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1.fa - | samtools sort - Sample_USBL-36I1-reads.end1.biaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_1038/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_1038-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_116/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_116-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_126/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_126-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_127/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_127-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_128/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_128-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_129/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_129-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_130/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_130-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_131/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_131-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_132/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_132-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_133/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_133-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_134/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_134-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_137/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_137-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_169/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_169-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_256-UB2/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_256-UB2-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_258-UB4/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_258-UB4-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_265/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_265-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_291/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_291-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_298/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_298-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_31/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_31-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_379/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_379-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_44/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_44-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_45/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_45-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_47/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_47-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_51/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_51-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_562alpha/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_562alpha-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_76/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_76-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_7K/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_7K-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_98/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_98-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_99/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_99-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A/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_A-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A30/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_A30-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_B/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_B-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C023/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_C023-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C033/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_C033-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C065/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_C065-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C083/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_C083-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C104/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_C104-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C119/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_C119-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C131/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_C131-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C147/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_C147-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_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_Canal-1I-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Indo1-7I/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_Indo1-7I-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M02/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_M02-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M03/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_M03-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M04/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_M04-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M05/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_M05-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_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_M08-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M09/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_M09-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M12/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_M12-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_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_M13-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_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_M15-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Moz13BIII/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_Moz13BIII-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_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_Peniche3I-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_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_TRB101-4-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_USBL-36I1/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_USBL-36I1-reads.end1.caudatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_1038/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_1038-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_116/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_116-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_126/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_126-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_127/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_127-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_128/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_128-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_129/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_129-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_130/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_130-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_131/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_131-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_132/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_132-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_133/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_133-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_134/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_134-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_137/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_137-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_169/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_169-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_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_16I-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_256-UB2/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_256-UB2-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_258-UB4/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_258-UB4-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_265/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_265-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_291/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_291-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_298/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_298-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_31/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_31-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_379/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_379-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_44/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_44-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_45/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_45-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_47/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_47-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_51/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_51-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_562alpha/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_562alpha-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_76/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_76-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_7K/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_7K-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_98/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_98-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_99/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_99-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A/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_A-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A30/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_A30-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_B/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_B-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C023/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_C023-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_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_C026-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C033/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_C033-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C065/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_C065-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C083/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_C083-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C104/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_C104-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C119/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_C119-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C131/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_C131-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C147/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_C147-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Indo1-7I/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_Indo1-7I-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M02/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_M02-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M03/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_M03-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M04/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_M04-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M05/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_M05-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M09/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_M09-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M12/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_M12-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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/2015-08-25-Paramecium-AS/RNA-editing; 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/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Moz13BIII/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_Moz13BIII-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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/2015-08-25-Paramecium-AS/RNA-editing; 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
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_USBL-36I1/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_USBL-36I1-reads.end1.multimicronucleatum.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_1038/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_1038-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_116/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_116-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_126/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_126-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_127/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_127-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_128/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_128-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_129/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_129-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_130/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_130-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_131/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_131-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_132/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_132-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_133/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_133-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_134/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_134-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_137/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_137-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_169/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_169-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_16I-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_256-UB2/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_256-UB2-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_258-UB4/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_258-UB4-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_265/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_265-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_291/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_291-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_298/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_298-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_31/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_31-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_379/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_379-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_44/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_44-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_45/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_45-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_47/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_47-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_51/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_51-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_562alpha/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_562alpha-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_76/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_76-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_7K/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_7K-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_98/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_98-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_99/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_99-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_A-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A30/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_A30-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_B/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_B-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C023/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_C023-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_C026-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C033/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_C033-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C065/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_C065-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C083/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_C083-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C104/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_C104-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C119/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_C119-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C131/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_C131-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C147/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_C147-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_Canal-1I-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Indo1-7I/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_Indo1-7I-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M02/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M02-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M03/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M03-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M04/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M04-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M05/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M05-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M08-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M09/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M09-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M12/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M12-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M13-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_M15-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Moz13BIII/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_Moz13BIII-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_Peniche3I-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_TRB101-4-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_USBL-36I1/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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf -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_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf.fa - | samtools sort - Sample_USBL-36I1-reads.end1.octaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_1038/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_1038-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_116/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_116-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_126/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_126-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_127/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_127-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_128/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_128-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_129/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_129-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_130/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_130-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_131/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_131-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_132/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_132-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_133/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_133-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_134/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_134-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_137/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_137-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_169/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_169-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_16I-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_256-UB2/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_256-UB2-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_258-UB4/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_258-UB4-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_265/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_265-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_291/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_291-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_298/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_298-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_31/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_31-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_379/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_379-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_44/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_44-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_45/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_45-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_47/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_47-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_51/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_51-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_562alpha/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_562alpha-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_76/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_76-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_7K/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_7K-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_98/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_98-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_99/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_99-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_A-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A30/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_A30-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_B/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_B-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C023/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_C023-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_C026-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C033/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_C033-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C065/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_C065-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C083/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_C083-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C104/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_C104-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C119/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_C119-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C131/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_C131-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C147/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_C147-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_Canal-1I-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Indo1-7I/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_Indo1-7I-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M02/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M02-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M03/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M03-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M04/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M04-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M05/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M05-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M08-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M09/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M09-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M12/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M12-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M13-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_M15-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Moz13BIII/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_Moz13BIII-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_Peniche3I-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_TRB101-4-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_USBL-36I1/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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft -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_pentaurelia_87E+87O/bowtie-indexes/pentaurelia_87E+87O_SOAPassembly_draft.fa - | samtools sort - Sample_USBL-36I1-reads.end1.pentaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_1038/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_1038-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_116/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_116-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_126/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_126-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_127/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_127-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_128/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_128-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_129/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_129-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_130/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_130-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_131/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_131-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_132/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_132-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_133/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_133-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_134/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_134-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_137/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_137-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_169/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_169-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_16I-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_256-UB2/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_256-UB2-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_258-UB4/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_258-UB4-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_265/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_265-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_291/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_291-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_298/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_298-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_31/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_31-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_379/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_379-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_44/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_44-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_45/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_45-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_47/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_47-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_51/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_51-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_562alpha/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_562alpha-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_76/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_76-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_7K/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_7K-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_98/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_98-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_99/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_99-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_A-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A30/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_A30-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_B/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_B-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C023/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_C023-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_C026-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C033/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_C033-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C065/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_C065-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C083/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_C083-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C104/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_C104-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C119/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_C119-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C131/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_C131-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C147/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_C147-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_Canal-1I-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Indo1-7I/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_Indo1-7I-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M02/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M02-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M03/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M03-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M04/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M04-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M05/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M05-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M08-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M09/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M09-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M12/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M12-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M13-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_M15-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Moz13BIII/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_Moz13BIII-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_Peniche3I-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_TRB101-4-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_USBL-36I1/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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_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_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1.fa - | samtools sort - Sample_USBL-36I1-reads.end1.primaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_1038/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_1038-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_116/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_116-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_126/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_126-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_127/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_127-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_128/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_128-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_129/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_129-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_130/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_130-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_131/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_131-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_132/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_132-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_133/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_133-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_134/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_134-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_137/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_137-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_169/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_169-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_16I-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_256-UB2/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_256-UB2-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_258-UB4/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_258-UB4-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_265/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_265-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_291/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_291-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_298/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_298-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_31/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_31-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_379/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_379-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_44/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_44-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_45/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_45-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_47/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_47-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_51/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_51-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_562alpha/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_562alpha-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_76/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_76-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_7K/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_7K-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_98/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_98-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_99/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_99-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_A-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A30/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_A30-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_B/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_B-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C023/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_C023-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_C026-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C033/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_C033-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C065/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_C065-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C083/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_C083-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C104/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_C104-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C119/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_C119-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C131/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_C131-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C147/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_C147-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_Canal-1I-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Indo1-7I/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_Indo1-7I-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M02/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M02-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M03/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M03-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M04/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M04-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M05/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M05-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M08-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M09/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M09-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M12/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M12-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M13-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_M15-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Moz13BIII/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_Moz13BIII-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_Peniche3I-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_TRB101-4-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_USBL-36I1/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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_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_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1.fa - | samtools sort - Sample_USBL-36I1-reads.end1.sexaurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_1038/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_1038-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_116/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_116-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_126/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_126-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_127/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_127-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_128/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_128-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_129/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_129-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_130/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_130-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_131/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_131-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_132/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_132-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_133/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_133-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_134/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_134-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_137/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_137-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_169/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_169-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_16I-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_256-UB2/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_256-UB2-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_258-UB4/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_258-UB4-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_265/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_265-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_291/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_291-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_298/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_298-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_31/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_31-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_379/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_379-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_44/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_44-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_45/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_45-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_47/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_47-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_51/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_51-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_562alpha/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_562alpha-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_76/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_76-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_7K/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_7K-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_98/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_98-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_99/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_99-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_A-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_A30/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_A30-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_B/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_B-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C023/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_C023-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_C026-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C033/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_C033-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C065/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_C065-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C083/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_C083-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C104/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_C104-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C119/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_C119-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C131/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_C131-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_C147/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_C147-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_Canal-1I-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Indo1-7I/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_Indo1-7I-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M02/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M02-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M03/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M03-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M04/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M04-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M05/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M05-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M08-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M09/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M09-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_M12/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M12-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M13-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_M15-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_Moz13BIII/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_Moz13BIII-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_Peniche3I-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; 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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_TRB101-4-reads.end1.tetraurelia.unique
cd /N/dc2/projects/marinovg/2015-08-25-Paramecium-AS/RNA-editing; zcat /N/dc2/projects/marinovg/Paramecium/variation/data/Sample_USBL-36I1/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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+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_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20+chrM.fa - | samtools sort - Sample_USBL-36I1-reads.end1.tetraurelia.unique