cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/53-Rhodospirillum_centenum_SW_uid58805; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR2094698 SRR2094699 SRR2094700 SRR2094701 | 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/Rhodospirillum_centenum_SW_uid58805/bowtie-indexes/NC_011420 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodospirillum_centenum_SW_uid58805/bowtie-indexes/NC_011420.fa - | samtools sort - CgrA.36mers.unique