cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/26-Myxococcus_xanthus; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1639662 | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Myxococcus_xanthus_DK_1622_uid58003/bowtie-indexes/NC_008095 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Myxococcus_xanthus_DK_1622_uid58003/bowtie-indexes/NC_008095.fa - | samtools sort - Control_sample.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/26-Myxococcus_xanthus; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1639666 | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Myxococcus_xanthus_DK_1622_uid58003/bowtie-indexes/NC_008095 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Myxococcus_xanthus_DK_1622_uid58003/bowtie-indexes/NC_008095.fa - | samtools sort - MrpC-sample1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/26-Myxococcus_xanthus; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1639664 | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Myxococcus_xanthus_DK_1622_uid58003/bowtie-indexes/NC_008095 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Myxococcus_xanthus_DK_1622_uid58003/bowtie-indexes/NC_008095.fa - | samtools sort - MrpC-sample2.36mers.unique