cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/52-Rhodobacter_capsulatus_SB1003; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1949994 | 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/Rhodobacter_capsulatus_SB_1003_uid47509/bowtie-indexes/NC_014034+NC_014035 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_capsulatus_SB_1003_uid47509/bowtie-indexes/NC_014034+NC_014035.fa - | samtools sort - FNR_input_R._capsulatus_replicate_3_ChIP-seq.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/52-Rhodobacter_capsulatus_SB1003; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1949992 | 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/Rhodobacter_capsulatus_SB_1003_uid47509/bowtie-indexes/NC_014034+NC_014035 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_capsulatus_SB_1003_uid47509/bowtie-indexes/NC_014034+NC_014035.fa - | samtools sort - FNR_input_R._capsulatus_replicate_1_ChIP-seq.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/52-Rhodobacter_capsulatus_SB1003; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1949991 | 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/Rhodobacter_capsulatus_SB_1003_uid47509/bowtie-indexes/NC_014034+NC_014035 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_capsulatus_SB_1003_uid47509/bowtie-indexes/NC_014034+NC_014035.fa - | samtools sort - FNR_overexpression_R._capsulatus_replicate_3_ChIP-seq.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/52-Rhodobacter_capsulatus_SB1003; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1949989 | 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/Rhodobacter_capsulatus_SB_1003_uid47509/bowtie-indexes/NC_014034+NC_014035 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_capsulatus_SB_1003_uid47509/bowtie-indexes/NC_014034+NC_014035.fa - | samtools sort - FNR_overexpression_R._capsulatus_replicate_1_ChIP-seq.36mers.unique