python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Abf1_X_ChIP_seq_20130118_9-GSM1647345/SRR1947833_1.fastq.gz Abf1_X_ChIP_seq_20130118_9-GSM1647345/SRR1947833_2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Abf1_X_ChIP_seq_20130118_9-GSM1647345/SRR1947833.2x25mers.unique