cd /N/dc2/projects/marinovg/reviews/15._2015_BMC_Bioinformatics_ChIP-seq_read_design/2016-02-10-CC-test; zcat GM12878-GTF2F1-ENCFF002ELJ-Rep2.end1.fastq.gz | 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/hg19/bowtie-indexes/hg19-male -p 16 -v 2 -k 2 -m 1 -t --best --strata -q --sam --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/hg19/sequence/hg19.fa - | samtools sort - GM12878-GTF2F1-ENCFF002ELJ-Rep2.36mers-end1.unique &
cd /N/dc2/projects/marinovg/reviews/15._2015_BMC_Bioinformatics_ChIP-seq_read_design/2016-02-10-CC-test; zcat GM12878-GTF2F1-ENCFF002ELJ-Rep2.end1.fastq.gz GM12878-GTF2F1-ENCFF002ELJ-Rep2.end2.fastq.gz | 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/hg19/bowtie-indexes/hg19-male -p 16 -v 2 -k 2 -m 1 -t --best --strata -q --sam --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/hg19/sequence/hg19.fa - | samtools sort - GM12878-GTF2F1-ENCFF002ELJ-Rep2.36mers-end1+2.unique &
cd /N/dc2/projects/marinovg/reviews/15._2015_BMC_Bioinformatics_ChIP-seq_read_design/2016-02-10-CC-test; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GM12878-GTF2F1-ENCFF002ELJ-Rep2.end1.fastq.gz GM12878-GTF2F1-ENCFF002ELJ-Rep2.end2.fastq.gz -trim 36 | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/hg19/bowtie-indexes/hg19-male -p 16 -v 2 -k 2 -m 1 -t --best --strata -q -X 1000 --sam --sam-nh --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/hg19/sequence/hg19.fa - | samtools sort - GM12878-GTF2F1-ENCFF002ELJ-Rep2.36mers-PE.unique &