cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/54-Pyrococcus_furiosus_DSM3638-ASM730v1; zcat ERR1059378.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic.fa - | samtools sort - pyruvate_1_input.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/54-Pyrococcus_furiosus_DSM3638-ASM730v1; zcat ERR1059379.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic.fa - | samtools sort - pyruvate_1_IP1-TrmBL1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/54-Pyrococcus_furiosus_DSM3638-ASM730v1; zcat ERR1059380.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic.fa - | samtools sort - pyruvate_1_IP2-TrmBL1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/54-Pyrococcus_furiosus_DSM3638-ASM730v1; zcat ERR1059381.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic.fa - | samtools sort - pyruvate_2_input.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/54-Pyrococcus_furiosus_DSM3638-ASM730v1; zcat ERR1059382.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic.fa - | samtools sort - pyruvate_2_IP1-TrmBL1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/54-Pyrococcus_furiosus_DSM3638-ASM730v1; zcat ERR1059383.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic.fa - | samtools sort - pyruvate_2_IP2-TrmBL1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/54-Pyrococcus_furiosus_DSM3638-ASM730v1; zcat ERR1059384.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic.fa - | samtools sort - starch_1_input.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/54-Pyrococcus_furiosus_DSM3638-ASM730v1; zcat ERR1059385.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic.fa - | samtools sort - starch_1_IP1-TrmBL1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/54-Pyrococcus_furiosus_DSM3638-ASM730v1; zcat ERR1059386.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pyrococcus_furiosus_DSM3638-ASM730v1/bowtie-indexes/GCA_000007305.1_ASM730v1_genomic.fa - | samtools sort - starch_1_IP2-TrmBL1.36mers.unique