zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-13189-rep2-JT_CTCFvalidationRNAseq_170303_S10.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-13190-rep1-JT_CTCFvalidationRNAseq_170303_S11.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-13190-rep2-JT_CTCFvalidationRNAseq_170303_S12.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-15171-rep1-JT_CTCFvalidationRNAseq_170303_S5.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-15171-rep2-JT_CTCFvalidationRNAseq_170303_S6.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-15173-rep1-JT_CTCFvalidationRNAseq_170303_S7.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-15173-rep2-JT_CTCFvalidationRNAseq_170303_S8.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-07-14-N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-12040-GH549_1_CTCFvalidationRNAseq_170812_S1.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-12040-GH549_2_CTCFvalidationRNAseq_170812_S2.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-12042-GH550_1_CTCFvalidationRNAseq_170812_S3.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-12042-GH550_2_CTCFvalidationRNAseq_170812_S4.1x50mers.a.e200.offrate1.bam
zcat 2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9.50mers.end1.fastq.gz 2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9.50mers.end2.fastq.gz | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9.1x50mers.a.e200.offrate1.bam
zcat 2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10.50mers.end1.fastq.gz 2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10.50mers.end2.fastq.gz | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10.1x50mers.a.e200.offrate1.bam
zcat 2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11.50mers.end1.fastq.gz 2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11.50mers.end2.fastq.gz | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11.1x50mers.a.e200.offrate1.bam
zcat 2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12.50mers.end1.fastq.gz 2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12.50mers.end2.fastq.gz | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-14376-GH551_1_CTCFvalidationRNAseq_170812_S5.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-14376-GH551_2_CTCFvalidationRNAseq_170812_S6.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-14377-GH552_1_CTCFvalidationRNAseq_170812_S7.1x50mers.a.e200.offrate1.bam
zcat 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 | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-14377-GH552_2_CTCFvalidationRNAseq_170812_S8.1x50mers.a.e200.offrate1.bam
zcat 2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13.50mers.end1.fastq.gz 2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13.50mers.end2.fastq.gz | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13.1x50mers.a.e200.offrate1.bam
zcat 2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14.50mers.end1.fastq.gz 2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14.50mers.end2.fastq.gz | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14.1x50mers.a.e200.offrate1.bam
zcat 2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15.50mers.end1.fastq.gz 2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15.50mers.end2.fastq.gz | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15.1x50mers.a.e200.offrate1.bam
zcat 2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16.50mers.end1.fastq.gz 2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16.50mers.end2.fastq.gz | python /home/users/marinovg/code/trimfastq.py - 50 -renameIDs read -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA -p 8 -e 200 -a --offrate 1 -t --sam - | samtools view -bT gencode.v19.annotation+homo_sapiens_SSU-LSU-rRNA.fa - -o 2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16.1x50mers.a.e200.offrate1.bam