zcat ABI3VP1_tnt.AT5G18090_col_a-GSM1925002/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ABI3VP1_tnt.AT5G18090_col_a-GSM1925002.50mers.TAIR10.unique
zcat ABI3VP1_tnt.AT5G25475_col_a-GSM1925003/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ABI3VP1_tnt.AT5G25475_col_a-GSM1925003.50mers.TAIR10.unique
zcat ABI3VP1_tnt.AT5G60130_col_a-GSM1925005/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ABI3VP1_tnt.AT5G60130_col_a-GSM1925005.50mers.TAIR10.unique
zcat ABI3VP1_tnt.AT5G60130_colamp_a-GSM1925004/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ABI3VP1_tnt.AT5G60130_colamp_a-GSM1925004.50mers.TAIR10.unique
zcat ABI3VP1_tnt.FUS3_col_a-GSM1925006/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ABI3VP1_tnt.FUS3_col_a-GSM1925006.50mers.TAIR10.unique
zcat ABI3VP1_tnt.NGA4_col_a-GSM1925007/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ABI3VP1_tnt.NGA4_col_a-GSM1925007.50mers.TAIR10.unique
zcat ABI3VP1_tnt.REM16_col_a-GSM1925008/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ABI3VP1_tnt.REM16_col_a-GSM1925008.50mers.TAIR10.unique
zcat ABI3VP1_tnt.VRN1_colamp_a-GSM1925009/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - ABI3VP1_tnt.VRN1_colamp_a-GSM1925009.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At1g19210_col_a-GSM1925033/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At1g19210_col_a-GSM1925033.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At1g19210_colamp_a-GSM1925032/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At1g19210_colamp_a-GSM1925032.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At1g22810_colamp_a-GSM1925034/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At1g22810_colamp_a-GSM1925034.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT1G28160_col_a-GSM1925020/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT1G28160_col_a-GSM1925020.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At1g36060_col_a-GSM1925036/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At1g36060_col_a-GSM1925036.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At1g36060_colamp_a-GSM1925035/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At1g36060_colamp_a-GSM1925035.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT1G44830_col_a-GSM1925021/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT1G44830_col_a-GSM1925021.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT1G71450_col_a-GSM1925023/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT1G71450_col_a-GSM1925023.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT1G71450_colamp_a-GSM1925022/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT1G71450_colamp_a-GSM1925022.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At1g75490_col_a-GSM1925038/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At1g75490_col_a-GSM1925038.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At1g75490_colamp_a-GSM1925037/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At1g75490_colamp_a-GSM1925037.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT1G77200_col_a-GSM1925025/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT1G77200_col_a-GSM1925025.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT1G77200_colamp_a-GSM1925024/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT1G77200_colamp_a-GSM1925024.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At1g77640_col_a-GSM1925039/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At1g77640_col_a-GSM1925039.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At2g33710_colamp_a-GSM1925040/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At2g33710_colamp_a-GSM1925040.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At2g44940_col_a-GSM1925042/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At2g44940_col_a-GSM1925042.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At2g44940_colamp_a-GSM1925041/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At2g44940_colamp_a-GSM1925041.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT3G16280_col_a-GSM1925027/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT3G16280_col_a-GSM1925027.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT3G16280_colamp_a-GSM1925026/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT3G16280_colamp_a-GSM1925026.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT3G57600_col_a-GSM1925028/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT3G57600_col_a-GSM1925028.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT3G60490_col_a-GSM1925030/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT3G60490_col_a-GSM1925030.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT3G60490_colamp_a-GSM1925029/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT3G60490_colamp_a-GSM1925029.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At4g16750_col_a-GSM1925044/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At4g16750_col_a-GSM1925044.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At4g16750_colamp_a-GSM1925043/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At4g16750_colamp_a-GSM1925043.50mers.TAIR10.unique
zcat AP2EREBP_tnt.AT4G18450_col_a-GSM1925031/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.AT4G18450_col_a-GSM1925031.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At4g28140_col_a-GSM1925046/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At4g28140_col_a-GSM1925046.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At4g28140_colamp_a-GSM1925045/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At4g28140_colamp_a-GSM1925045.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At4g31060_col_a-GSM1925048/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At4g31060_col_a-GSM1925048.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At4g31060_colamp_a-GSM1925047/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At4g31060_colamp_a-GSM1925047.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At4g32800_colamp_a-GSM1925049/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At4g32800_colamp_a-GSM1925049.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At5g18450_col_a-GSM1925050/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At5g18450_col_a-GSM1925050.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At5g65130_col_a-GSM1925052/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At5g65130_col_a-GSM1925052.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At5g65130_colamp_a-GSM1925051/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At5g65130_colamp_a-GSM1925051.50mers.TAIR10.unique
zcat AP2EREBP_tnt.At5g67000_col_a-GSM1925053/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.At5g67000_col_a-GSM1925053.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CBF1_col_a-GSM1925055/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CBF1_col_a-GSM1925055.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CBF1_colamp_a-GSM1925054/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CBF1_colamp_a-GSM1925054.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CBF2_col_a-GSM1925057/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CBF2_col_a-GSM1925057.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CBF2_colamp_a-GSM1925056/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CBF2_colamp_a-GSM1925056.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CBF3_col_a-GSM1925059/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CBF3_col_a-GSM1925059.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CBF3_colamp_a-GSM1925058/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CBF3_colamp_a-GSM1925058.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CBF4_col_a-GSM1925061/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CBF4_col_a-GSM1925061.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CBF4_colamp_a-GSM1925060/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CBF4_colamp_a-GSM1925060.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CEJ1_col_a-GSM1925063/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CEJ1_col_a-GSM1925063.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CEJ1_colamp_a-GSM1925062/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CEJ1_colamp_a-GSM1925062.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CRF10_col100_a-GSM1925064/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CRF10_col100_a-GSM1925064.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CRF10_colamp_a-GSM1925065/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CRF10_colamp_a-GSM1925065.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CRF4_col_a-GSM1925067/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CRF4_col_a-GSM1925067.50mers.TAIR10.unique
zcat AP2EREBP_tnt.CRF4_colamp_a-GSM1925066/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.CRF4_colamp_a-GSM1925066.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DDF1_col_a-GSM1925069/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DDF1_col_a-GSM1925069.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DDF1_colamp_a-GSM1925068/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DDF1_colamp_a-GSM1925068.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DDF2_col_a-GSM1925070/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DDF2_col_a-GSM1925070.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DEAR2_col_a-GSM1925072/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DEAR2_col_a-GSM1925072.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DEAR2_colamp_a-GSM1925071/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DEAR2_colamp_a-GSM1925071.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DEAR3_col_a-GSM1925074/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DEAR3_col_a-GSM1925074.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DEAR3_colamp_a-GSM1925073/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DEAR3_colamp_a-GSM1925073.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DEAR5_col_a-GSM1925076/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DEAR5_col_a-GSM1925076.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DEAR5_colamp_a-GSM1925075/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DEAR5_colamp_a-GSM1925075.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DREB19_col_a-GSM1925078/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DREB19_col_a-GSM1925078.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DREB19_colamp_a-GSM1925077/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DREB19_colamp_a-GSM1925077.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DREB26_col_a-GSM1925081/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DREB26_col_a-GSM1925081.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DREB2_col_a-GSM1925080/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DREB2_col_a-GSM1925080.50mers.TAIR10.unique
zcat AP2EREBP_tnt.DREB2_colamp_a-GSM1925079/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.DREB2_colamp_a-GSM1925079.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF104_col_a-GSM1925087/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF104_col_a-GSM1925087.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF104_colamp_a-GSM1925086/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF104_colamp_a-GSM1925086.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF105_colamp_a-GSM1925088/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF105_colamp_a-GSM1925088.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF10_col_a-GSM1925085*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF10_col_a-GSM1925085.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF10_colamp_a-GSM1925084/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF10_colamp_a-GSM1925084.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF115_col_a-GSM1925092/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF115_col_a-GSM1925092.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF115_colamp_a-GSM1925091/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF115_colamp_a-GSM1925091.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF11_colamp_a-GSM1925089/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF11_colamp_a-GSM1925089.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF11_col_b-GSM1925090/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF11_col_b-GSM1925090.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF13_colamp_a-GSM1925093/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF13_colamp_a-GSM1925093.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF13_col_b-GSM1925094/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF13_col_b-GSM1925094.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF15_colamp_a-GSM1925095/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF15_colamp_a-GSM1925095.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF1_col_a-GSM1925083/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF1_col_a-GSM1925083.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF1_colamp_a-GSM1925082/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF1_colamp_a-GSM1925082.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF2_col_a-GSM1925097/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF2_col_a-GSM1925097.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF2_colamp_a-GSM1925096/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF2_colamp_a-GSM1925096.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF3_col_a-GSM1925099/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF3_col_a-GSM1925099.50mers.TAIR10.unique
zcat AP2EREBP_tnt.ERF3_colamp_a-GSM1925098/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - AP2EREBP_tnt.ERF3_colamp_a-GSM1925098.50mers.TAIR10.unique
zcat control_none.beads_col_v3a-GSM1924998/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - control_none.beads_col_v3a-GSM1924998.50mers.TAIR10.unique
zcat control_tnt-pixhalo_colamp_v3a-GSM1924999/*_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/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 --k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - control_tnt-pixhalo_colamp_v3a-GSM1924999.50mers.TAIR10.unique