cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/29-Streptomyces_coelicolor; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1503874 | 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/Streptomyces_coelicolor_A3_2__uid57801/bowtie-indexes/all -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Streptomyces_coelicolor_A3_2__uid57801/bowtie-indexes/all.fa - | samtools sort - NdgR.36mers.unique