cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/57-Waddlia_chondrophila_WSU_86_1044_uid49531; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1981513 | 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/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226.fa - | samtools sort - HrcA_72h-GSM1661998.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/57-Waddlia_chondrophila_WSU_86_1044_uid49531; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1981514 | 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/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226.fa - | samtools sort - Wcw_1671_EB-GSM1661999.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/57-Waddlia_chondrophila_WSU_86_1044_uid49531; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1981515 | 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/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226.fa - | samtools sort - Euo_72h-GSM1662000.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/57-Waddlia_chondrophila_WSU_86_1044_uid49531; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1981516 | 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/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226.fa - | samtools sort - PhoB_EB-GSM1662001.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/57-Waddlia_chondrophila_WSU_86_1044_uid49531; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1981517 | 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/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226.fa - | samtools sort - Wcw_1223_56h-GSM1662002.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/57-Waddlia_chondrophila_WSU_86_1044_uid49531; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1981518 | 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/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226.fa - | samtools sort - ParB_EB-GSM1662003.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/57-Waddlia_chondrophila_WSU_86_1044_uid49531; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1981519 | 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/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226.fa - | samtools sort - NrdR_EB-GSM1662004.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/57-Waddlia_chondrophila_WSU_86_1044_uid49531; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1981520 | 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/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226.fa - | samtools sort - AtoC_EB-GSM1662005.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/57-Waddlia_chondrophila_WSU_86_1044_uid49531; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1981521 | 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/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226.fa - | samtools sort - DnaA3_24h-GSM1662006.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/57-Waddlia_chondrophila_WSU_86_1044_uid49531; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1981522 | 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/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Waddlia_chondrophila_WSU_86_1044_uid49531/bowtie-indexes/NC_014225+NC_014226.fa - | samtools sort - DnaA1_72h-GSM1662007.36mers.unique