cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/35-Bacillus_subtilis_subsp._subtilis_str._AG1839; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1509766 SRR1509767 SRR1509768 SRR1509769 SRR1509770 SRR1509771 SRR1509772 SRR1509773 SRR1509775 SRR1509776 SRR1509777 SRR1509779  | 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/Bacillus_subtilis_subsp._subtilis_str._AG1839/bowtie-indexes/GCA_000699525.1_ASM69952v1_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Bacillus_subtilis_subsp._subtilis_str._AG1839/bowtie-indexes/GCA_000699525.1_ASM69952v1_genomic.fa - | samtools sort - DnaA-IDAP-Seq.36mers.unique