cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/27-Pseudomonas_fluorescens_F113; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1184483 | 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/Pseudomonas_fluorescens_F113_uid87037/bowtie-indexes/NC_016830 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Pseudomonas_fluorescens_F113_uid87037/bowtie-indexes/NC_016830.fa - | samtools sort - AmrZ.36mers.unique