bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L110-CRISPRa-CTCF_N4293-Input\tPL:Illumina"  L110-CRISPRa-CTCF_N4293-Input.trimmed_renamed.end1.fastq L110-CRISPRa-CTCF_N4293-Input.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L110-CRISPRa-CTCF_N4293-Input.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L111-CRISPRk-CTCF_N4293-Input\tPL:Illumina"  L111-CRISPRk-CTCF_N4293-Input.trimmed_renamed.end1.fastq L111-CRISPRk-CTCF_N4293-Input.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L111-CRISPRk-CTCF_N4293-Input.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L112-CRISPRi-CTCF_N4293-Input\tPL:Illumina"  L112-CRISPRi-CTCF_N4293-Input.trimmed_renamed.end1.fastq L112-CRISPRi-CTCF_N4293-Input.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L112-CRISPRi-CTCF_N4293-Input.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L115-CRISPRa-CTCF_7140-CTCF\tPL:Illumina"  L115-CRISPRa-CTCF_7140-CTCF.trimmed_renamed.end1.fastq L115-CRISPRa-CTCF_7140-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L115-CRISPRa-CTCF_7140-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L116-CRISPRa-CTCF_11698-CTCF\tPL:Illumina"  L116-CRISPRa-CTCF_11698-CTCF.trimmed_renamed.end1.fastq L116-CRISPRa-CTCF_11698-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L116-CRISPRa-CTCF_11698-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L117-CRISPRa-CTCF_13189-CTCF\tPL:Illumina"  L117-CRISPRa-CTCF_13189-CTCF.trimmed_renamed.end1.fastq L117-CRISPRa-CTCF_13189-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L117-CRISPRa-CTCF_13189-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L118-CRISPRa-CTCF_15173-CTCF\tPL:Illumina"  L118-CRISPRa-CTCF_15173-CTCF.trimmed_renamed.end1.fastq L118-CRISPRa-CTCF_15173-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L118-CRISPRa-CTCF_15173-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L119-CRISPRa-CTCF_N4293-CTCF\tPL:Illumina"  L119-CRISPRa-CTCF_N4293-CTCF.trimmed_renamed.end1.fastq L119-CRISPRa-CTCF_N4293-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L119-CRISPRa-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L120-CRISPRk-CTCF_N4293-CTCF\tPL:Illumina"  L120-CRISPRk-CTCF_N4293-CTCF.trimmed_renamed.end1.fastq L120-CRISPRk-CTCF_N4293-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L120-CRISPRk-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L121-CRISPRk-CTCF_8005-CTCF\tPL:Illumina"  L121-CRISPRk-CTCF_8005-CTCF.trimmed_renamed.end1.fastq L121-CRISPRk-CTCF_8005-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L121-CRISPRk-CTCF_8005-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L122-CRISPRk-CTCF_12040-CTCF\tPL:Illumina"  L122-CRISPRk-CTCF_12040-CTCF.trimmed_renamed.end1.fastq L122-CRISPRk-CTCF_12040-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L122-CRISPRk-CTCF_12040-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L123-CRISPRk-CTCF_13004-CTCF\tPL:Illumina"  L123-CRISPRk-CTCF_13004-CTCF.trimmed_renamed.end1.fastq L123-CRISPRk-CTCF_13004-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L123-CRISPRk-CTCF_13004-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L124-CRISPRk-CTCF_14259-CTCF\tPL:Illumina"  L124-CRISPRk-CTCF_14259-CTCF.trimmed_renamed.end1.fastq L124-CRISPRk-CTCF_14259-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L124-CRISPRk-CTCF_14259-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L125-CRISPRk-CTCF_14376-CTCF\tPL:Illumina"  L125-CRISPRk-CTCF_14376-CTCF.trimmed_renamed.end1.fastq L125-CRISPRk-CTCF_14376-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L125-CRISPRk-CTCF_14376-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L126-CRISPRk-CTCF_15776-CTCF\tPL:Illumina"  L126-CRISPRk-CTCF_15776-CTCF.trimmed_renamed.end1.fastq L126-CRISPRk-CTCF_15776-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L126-CRISPRk-CTCF_15776-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L127-CRISPRi-CTCF_5635-CTCF\tPL:Illumina"  L127-CRISPRi-CTCF_5635-CTCF.trimmed_renamed.end1.fastq L127-CRISPRi-CTCF_5635-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L127-CRISPRi-CTCF_5635-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L128-CRISPRi-CTCF_15923-CTCF\tPL:Illumina"  L128-CRISPRi-CTCF_15923-CTCF.trimmed_renamed.end1.fastq L128-CRISPRi-CTCF_15923-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L128-CRISPRi-CTCF_15923-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L129-CRISPRi-CTCF_8004-CTCF\tPL:Illumina"  L129-CRISPRi-CTCF_8004-CTCF.trimmed_renamed.end1.fastq L129-CRISPRi-CTCF_8004-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L129-CRISPRi-CTCF_8004-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync
bwa mem -t 8 -M ~/genomes/hg19/bwa-indexes/hg19-female.fa -R "@RG\tID:FCC1N99ACXX:8:1101:1551:2189#GCCAATAT\tSM:L130-CRISPRi-CTCF_N4293-CTCF\tPL:Illumina"  L130-CRISPRi-CTCF_N4293-CTCF.trimmed_renamed.end1.fastq L130-CRISPRi-CTCF_N4293-CTCF.trimmed_renamed.end2.fastq | ~/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT ~/genomes/hg19/sequence/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L130-CRISPRi-CTCF_N4293-CTCF.2x75mers-trimmed.bwa-mem.hg19-female && sync