zcat Control_4_FGFR1_GSM2439179/SRR5128177_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_4_FGFR1_GSM2439179.1x50mers.chrM.unique
zcat Control_4_input-GSM2439178/SRR5128176_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_4_input-GSM2439178.1x50mers.chrM.unique
zcat Patient_3_FGFR1_GSM2439181/SRR5128179_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Patient_3_FGFR1_GSM2439181.1x50mers.chrM.unique
zcat Patient_3_input-GSM2439180/SRR5128178_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Patient_3_input-GSM2439180.1x50mers.chrM.unique
zcat Patient_3_NOTCH_-GSM2439182/SRR5128180_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM -p 20 -v 1 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep chrM | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Patient_3_NOTCH_-GSM2439182.1x50mers.chrM.unique
zcat Control_4_FGFR1_GSM2439179/SRR5128177_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep hg38-no-haps | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_4_FGFR1_GSM2439179.1x50mers.hg38-no-haps.unique
zcat Control_4_input-GSM2439178/SRR5128176_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep hg38-no-haps | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Control_4_input-GSM2439178.1x50mers.hg38-no-haps.unique
zcat Patient_3_FGFR1_GSM2439181/SRR5128179_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep hg38-no-haps | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Patient_3_FGFR1_GSM2439181.1x50mers.hg38-no-haps.unique
zcat Patient_3_input-GSM2439180/SRR5128178_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep hg38-no-haps | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Patient_3_input-GSM2439180.1x50mers.hg38-no-haps.unique
zcat Patient_3_NOTCH_-GSM2439182/SRR5128180_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 50 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-no-haps -p 20 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | grep hg38-no-haps | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Patient_3_NOTCH_-GSM2439182.1x50mers.hg38-no-haps.unique