python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-13004-rep1-S1.50mers.end1.fastq.gz 2017-07-14-13004-rep1-S1.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-13004-rep1-S1-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-13004-rep2-S2.50mers.end1.fastq.gz 2017-07-14-13004-rep2-S2.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-13004-rep2-S2-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-13006-rep1-S3.50mers.end1.fastq.gz 2017-07-14-13006-rep1-S3.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-13006-rep1-S3-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-13006-rep2-S4.50mers.end1.fastq.gz 2017-07-14-13006-rep2-S4.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-13006-rep2-S4-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9.50mers.end1.fastq.gz 2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-13189-rep2-JT_CTCFvalidationRNAseq_170303_S10.50mers.end1.fastq.gz 2017-07-14-13189-rep2-JT_CTCFvalidationRNAseq_170303_S10.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-13189-rep2-JT_CTCFvalidationRNAseq_170303_S10-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-13190-rep1-JT_CTCFvalidationRNAseq_170303_S11.50mers.end1.fastq.gz 2017-07-14-13190-rep1-JT_CTCFvalidationRNAseq_170303_S11.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-13190-rep1-JT_CTCFvalidationRNAseq_170303_S11-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-13190-rep2-JT_CTCFvalidationRNAseq_170303_S12.50mers.end1.fastq.gz 2017-07-14-13190-rep2-JT_CTCFvalidationRNAseq_170303_S12.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-13190-rep2-JT_CTCFvalidationRNAseq_170303_S12-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-15171-rep1-JT_CTCFvalidationRNAseq_170303_S5.50mers.end1.fastq.gz 2017-07-14-15171-rep1-JT_CTCFvalidationRNAseq_170303_S5.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-15171-rep1-JT_CTCFvalidationRNAseq_170303_S5-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-15171-rep2-JT_CTCFvalidationRNAseq_170303_S6.50mers.end1.fastq.gz 2017-07-14-15171-rep2-JT_CTCFvalidationRNAseq_170303_S6.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-15171-rep2-JT_CTCFvalidationRNAseq_170303_S6-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-15173-rep1-JT_CTCFvalidationRNAseq_170303_S7.50mers.end1.fastq.gz 2017-07-14-15173-rep1-JT_CTCFvalidationRNAseq_170303_S7.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-15173-rep1-JT_CTCFvalidationRNAseq_170303_S7-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-15173-rep2-JT_CTCFvalidationRNAseq_170303_S8.50mers.end1.fastq.gz 2017-07-14-15173-rep2-JT_CTCFvalidationRNAseq_170303_S8.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-15173-rep2-JT_CTCFvalidationRNAseq_170303_S8-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1.50mers.end1.fastq.gz 2017-07-14-N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-N4293-rep1-S5.50mers.end1.fastq.gz 2017-07-14-N4293-rep1-S5.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-N4293-rep1-S5-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-N4293-rep1-S5.50mers.end1.fastq.gz 2017-07-14-N4293-rep1-S5.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-N4293-rep1-S5-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2.50mers.end1.fastq.gz 2017-07-14-N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3.50mers.end1.fastq.gz 2017-07-14-N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-N4371-rep1-S7.50mers.end1.fastq.gz 2017-07-14-N4371-rep1-S7.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-N4371-rep1-S7-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4.50mers.end1.fastq.gz 2017-07-14-N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-07-14-N4371-rep2-S8.50mers.end1.fastq.gz 2017-07-14-N4371-rep2-S8.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-07-14-N4371-rep2-S8-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-12040-GH549_1_CTCFvalidationRNAseq_170812_S1.50mers.end1.fastq.gz 2017-08-14-12040-GH549_1_CTCFvalidationRNAseq_170812_S1.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-12040-GH549_1_CTCFvalidationRNAseq_170812_S1-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-12040-GH549_2_CTCFvalidationRNAseq_170812_S2.50mers.end1.fastq.gz 2017-08-14-12040-GH549_2_CTCFvalidationRNAseq_170812_S2.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-12040-GH549_2_CTCFvalidationRNAseq_170812_S2-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-12042-GH550_1_CTCFvalidationRNAseq_170812_S3.50mers.end1.fastq.gz 2017-08-14-12042-GH550_1_CTCFvalidationRNAseq_170812_S3.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-12042-GH550_1_CTCFvalidationRNAseq_170812_S3-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-12042-GH550_2_CTCFvalidationRNAseq_170812_S4.50mers.end1.fastq.gz 2017-08-14-12042-GH550_2_CTCFvalidationRNAseq_170812_S4.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-12042-GH550_2_CTCFvalidationRNAseq_170812_S4-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9.50mers.end1.fastq.gz 2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10.50mers.end1.fastq.gz 2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11.50mers.end1.fastq.gz 2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12.50mers.end1.fastq.gz 2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-14376-GH551_1_CTCFvalidationRNAseq_170812_S5.50mers.end1.fastq.gz 2017-08-14-14376-GH551_1_CTCFvalidationRNAseq_170812_S5.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-14376-GH551_1_CTCFvalidationRNAseq_170812_S5-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-14376-GH551_2_CTCFvalidationRNAseq_170812_S6.50mers.end1.fastq.gz 2017-08-14-14376-GH551_2_CTCFvalidationRNAseq_170812_S6.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-14376-GH551_2_CTCFvalidationRNAseq_170812_S6-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-14377-GH552_1_CTCFvalidationRNAseq_170812_S7.50mers.end1.fastq.gz 2017-08-14-14377-GH552_1_CTCFvalidationRNAseq_170812_S7.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-14377-GH552_1_CTCFvalidationRNAseq_170812_S7-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-14377-GH552_2_CTCFvalidationRNAseq_170812_S8.50mers.end1.fastq.gz 2017-08-14-14377-GH552_2_CTCFvalidationRNAseq_170812_S8.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-14377-GH552_2_CTCFvalidationRNAseq_170812_S8-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13.50mers.end1.fastq.gz 2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14.50mers.end1.fastq.gz 2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15.50mers.end1.fastq.gz 2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py 2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16.50mers.end1.fastq.gz 2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16.50mers.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03 -p 8 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation+humrep_RepBase16.03.fa - -o 2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16-2x50mers.GENCODEV25+humrep_RepBase16.03.a.e200.offrate1.bam