cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/28-Anabaena_sp._PCC_7120; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1463356 | 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/Anabaena_sp._PCC_7120/bowtie-indexes/GCA_000009705.1_ASM970v1_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/Anabaena_sp._PCC_7120/bowtie-indexes/GCA_000009705.1_ASM970v1_genomic.fa - | samtools sort - PacR-All3953-CSS57-Input-GSM1420986.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/28-Anabaena_sp._PCC_7120; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1463357 | 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/Anabaena_sp._PCC_7120/bowtie-indexes/GCA_000009705.1_ASM970v1_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/Anabaena_sp._PCC_7120/bowtie-indexes/GCA_000009705.1_ASM970v1_genomic.fa - | samtools sort - PacR-All3953-CSS57-ChIP-GSM1420987.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/28-Anabaena_sp._PCC_7120; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1463358 | 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/Anabaena_sp._PCC_7120/bowtie-indexes/GCA_000009705.1_ASM970v1_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/Anabaena_sp._PCC_7120/bowtie-indexes/GCA_000009705.1_ASM970v1_genomic.fa - | samtools sort - PacR-All3953-CSS68-Input-GSM1420988.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/28-Anabaena_sp._PCC_7120; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1463359 | 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/Anabaena_sp._PCC_7120/bowtie-indexes/GCA_000009705.1_ASM970v1_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/Anabaena_sp._PCC_7120/bowtie-indexes/GCA_000009705.1_ASM970v1_genomic.fa - | samtools sort - PacR-All3953-CSS68-ChIP-GSM1420989.36mers.unique