~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L225-K562-CRISPRi-15776-a.end1.36mers.fastq.gz L225-K562-CRISPRi-15776-a.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L225-K562-CRISPRi-15776-a.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L226-K562-CRISPRi-15776-b.end1.36mers.fastq.gz L226-K562-CRISPRi-15776-b.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L226-K562-CRISPRi-15776-b.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L227-K562-CRISPRi-15777-a.end1.36mers.fastq.gz L227-K562-CRISPRi-15777-a.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L227-K562-CRISPRi-15777-a.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L228-K562-CRISPRi-15777-b.end1.36mers.fastq.gz L228-K562-CRISPRi-15777-b.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L228-K562-CRISPRi-15777-b.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L223-K562-CRISPRi-N-a.end1.36mers.fastq.gz L223-K562-CRISPRi-N-a.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L223-K562-CRISPRi-N-a.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L224-K562-CRISPRi-N-b.end1.36mers.fastq.gz L224-K562-CRISPRi-N-b.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L224-K562-CRISPRi-N-b.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L229-K562-CRISPRk-N-a.end1.36mers.fastq.gz L229-K562-CRISPRk-N-a.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L229-K562-CRISPRk-N-a.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L230-K562-CRISPRk-N-b.end1.36mers.fastq.gz L230-K562-CRISPRk-N-b.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L230-K562-CRISPRk-N-b.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L231-K562-CRISPRk-15776-a.end1.36mers.fastq.gz L231-K562-CRISPRk-15776-a.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L231-K562-CRISPRk-15776-a.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L232-K562-CRISPRk-15776-b.end1.36mers.fastq.gz L232-K562-CRISPRk-15776-b.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L232-K562-CRISPRk-15776-b.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L233-K562-CRISPRk-15777-a.end1.36mers.fastq.gz L233-K562-CRISPRk-15777-a.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L233-K562-CRISPRk-15777-a.2x36mers.hg19-female.bwa
~/programs/bwa-0.7.5a/bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa L234-K562-CRISPRk-15777-b.end1.36mers.fastq.gz L234-K562-CRISPRk-15777-b.end2.36mers.fastq.gz | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L234-K562-CRISPRk-15777-b.2x36mers.hg19-female.bwa