python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-13004-rep1-S1.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep2-S2-2x50mers-STAR2.5.3a-GENCODEV19/13004-2_S2_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep2-S2-2x50mers-STAR2.5.3a-GENCODEV19/13004-2_S2_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep2-S2-2x50mers-STAR2.5.3a-GENCODEV19/13004-2_S2_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep2-S2-2x50mers-STAR2.5.3a-GENCODEV19/13004-2_S2_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-13004-rep2-S2.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13006-rep1-S3-2x50mers-STAR2.5.3a-GENCODEV19/13006-1_S3_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13006-rep1-S3-2x50mers-STAR2.5.3a-GENCODEV19/13006-1_S3_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13006-rep1-S3-2x50mers-STAR2.5.3a-GENCODEV19/13006-1_S3_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13006-rep1-S3-2x50mers-STAR2.5.3a-GENCODEV19/13006-1_S3_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-13006-rep1-S3.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13006-rep2-S4-2x50mers-STAR2.5.3a-GENCODEV19/13006-2_S4_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13006-rep2-S4-2x50mers-STAR2.5.3a-GENCODEV19/13006-2_S4_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13006-rep2-S4-2x50mers-STAR2.5.3a-GENCODEV19/13006-2_S4_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13006-rep2-S4-2x50mers-STAR2.5.3a-GENCODEV19/13006-2_S4_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-13006-rep2-S4.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9-2x50mers-STAR2.5.3a-GENCODEV19/13189-1_JT_CTCFvalidationRNAseq_170303_S9_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9-2x50mers-STAR2.5.3a-GENCODEV19/13189-1_JT_CTCFvalidationRNAseq_170303_S9_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9-2x50mers-STAR2.5.3a-GENCODEV19/13189-1_JT_CTCFvalidationRNAseq_170303_S9_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9-2x50mers-STAR2.5.3a-GENCODEV19/13189-1_JT_CTCFvalidationRNAseq_170303_S9_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-13189-rep1-JT_CTCFvalidationRNAseq_170303_S9.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13189-rep2-JT_CTCFvalidationRNAseq_170303_S10-2x50mers-STAR2.5.3a-GENCODEV19/13189-2_JT_CTCFvalidationRNAseq_170303_S10_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13189-rep2-JT_CTCFvalidationRNAseq_170303_S10-2x50mers-STAR2.5.3a-GENCODEV19/13189-2_JT_CTCFvalidationRNAseq_170303_S10_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13189-rep2-JT_CTCFvalidationRNAseq_170303_S10-2x50mers-STAR2.5.3a-GENCODEV19/13189-2_JT_CTCFvalidationRNAseq_170303_S10_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13189-rep2-JT_CTCFvalidationRNAseq_170303_S10-2x50mers-STAR2.5.3a-GENCODEV19/13189-2_JT_CTCFvalidationRNAseq_170303_S10_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-13189-rep2-JT_CTCFvalidationRNAseq_170303_S10.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13190-rep1-JT_CTCFvalidationRNAseq_170303_S11-2x50mers-STAR2.5.3a-GENCODEV19/13190-1_JT_CTCFvalidationRNAseq_170303_S11_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13190-rep1-JT_CTCFvalidationRNAseq_170303_S11-2x50mers-STAR2.5.3a-GENCODEV19/13190-1_JT_CTCFvalidationRNAseq_170303_S11_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13190-rep1-JT_CTCFvalidationRNAseq_170303_S11-2x50mers-STAR2.5.3a-GENCODEV19/13190-1_JT_CTCFvalidationRNAseq_170303_S11_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13190-rep1-JT_CTCFvalidationRNAseq_170303_S11-2x50mers-STAR2.5.3a-GENCODEV19/13190-1_JT_CTCFvalidationRNAseq_170303_S11_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-13190-rep1-JT_CTCFvalidationRNAseq_170303_S11.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13190-rep2-JT_CTCFvalidationRNAseq_170303_S12-2x50mers-STAR2.5.3a-GENCODEV19/13190-2_JT_CTCFvalidationRNAseq_170303_S12_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13190-rep2-JT_CTCFvalidationRNAseq_170303_S12-2x50mers-STAR2.5.3a-GENCODEV19/13190-2_JT_CTCFvalidationRNAseq_170303_S12_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13190-rep2-JT_CTCFvalidationRNAseq_170303_S12-2x50mers-STAR2.5.3a-GENCODEV19/13190-2_JT_CTCFvalidationRNAseq_170303_S12_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13190-rep2-JT_CTCFvalidationRNAseq_170303_S12-2x50mers-STAR2.5.3a-GENCODEV19/13190-2_JT_CTCFvalidationRNAseq_170303_S12_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-13190-rep2-JT_CTCFvalidationRNAseq_170303_S12.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15171-rep1-JT_CTCFvalidationRNAseq_170303_S5-2x50mers-STAR2.5.3a-GENCODEV19/15171-1_JT_CTCFvalidationRNAseq_170303_S5_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15171-rep1-JT_CTCFvalidationRNAseq_170303_S5-2x50mers-STAR2.5.3a-GENCODEV19/15171-1_JT_CTCFvalidationRNAseq_170303_S5_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15171-rep1-JT_CTCFvalidationRNAseq_170303_S5-2x50mers-STAR2.5.3a-GENCODEV19/15171-1_JT_CTCFvalidationRNAseq_170303_S5_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15171-rep1-JT_CTCFvalidationRNAseq_170303_S5-2x50mers-STAR2.5.3a-GENCODEV19/15171-1_JT_CTCFvalidationRNAseq_170303_S5_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-15171-rep1-JT_CTCFvalidationRNAseq_170303_S5.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15171-rep2-JT_CTCFvalidationRNAseq_170303_S6-2x50mers-STAR2.5.3a-GENCODEV19/15171-2_JT_CTCFvalidationRNAseq_170303_S6_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15171-rep2-JT_CTCFvalidationRNAseq_170303_S6-2x50mers-STAR2.5.3a-GENCODEV19/15171-2_JT_CTCFvalidationRNAseq_170303_S6_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15171-rep2-JT_CTCFvalidationRNAseq_170303_S6-2x50mers-STAR2.5.3a-GENCODEV19/15171-2_JT_CTCFvalidationRNAseq_170303_S6_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15171-rep2-JT_CTCFvalidationRNAseq_170303_S6-2x50mers-STAR2.5.3a-GENCODEV19/15171-2_JT_CTCFvalidationRNAseq_170303_S6_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-15171-rep2-JT_CTCFvalidationRNAseq_170303_S6.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15173-rep1-JT_CTCFvalidationRNAseq_170303_S7-2x50mers-STAR2.5.3a-GENCODEV19/15173-1_JT_CTCFvalidationRNAseq_170303_S7_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15173-rep1-JT_CTCFvalidationRNAseq_170303_S7-2x50mers-STAR2.5.3a-GENCODEV19/15173-1_JT_CTCFvalidationRNAseq_170303_S7_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15173-rep1-JT_CTCFvalidationRNAseq_170303_S7-2x50mers-STAR2.5.3a-GENCODEV19/15173-1_JT_CTCFvalidationRNAseq_170303_S7_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15173-rep1-JT_CTCFvalidationRNAseq_170303_S7-2x50mers-STAR2.5.3a-GENCODEV19/15173-1_JT_CTCFvalidationRNAseq_170303_S7_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-15173-rep1-JT_CTCFvalidationRNAseq_170303_S7.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15173-rep2-JT_CTCFvalidationRNAseq_170303_S8-2x50mers-STAR2.5.3a-GENCODEV19/15173-2_JT_CTCFvalidationRNAseq_170303_S8_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15173-rep2-JT_CTCFvalidationRNAseq_170303_S8-2x50mers-STAR2.5.3a-GENCODEV19/15173-2_JT_CTCFvalidationRNAseq_170303_S8_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15173-rep2-JT_CTCFvalidationRNAseq_170303_S8-2x50mers-STAR2.5.3a-GENCODEV19/15173-2_JT_CTCFvalidationRNAseq_170303_S8_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-15173-rep2-JT_CTCFvalidationRNAseq_170303_S8-2x50mers-STAR2.5.3a-GENCODEV19/15173-2_JT_CTCFvalidationRNAseq_170303_S8_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-15173-rep2-JT_CTCFvalidationRNAseq_170303_S8.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1-2x50mers-STAR2.5.3a-GENCODEV19/N4293-1_JT_CTCFvalidationRNAseq_170303_S1_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1-2x50mers-STAR2.5.3a-GENCODEV19/N4293-1_JT_CTCFvalidationRNAseq_170303_S1_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1-2x50mers-STAR2.5.3a-GENCODEV19/N4293-1_JT_CTCFvalidationRNAseq_170303_S1_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1-2x50mers-STAR2.5.3a-GENCODEV19/N4293-1_JT_CTCFvalidationRNAseq_170303_S1_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-N4293-rep1-JT_CTCFvalidationRNAseq_170303_S1.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-S5-2x50mers-STAR2.5.3a-GENCODEV19/N4293-1_S5_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-S5-2x50mers-STAR2.5.3a-GENCODEV19/N4293-1_S5_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-S5-2x50mers-STAR2.5.3a-GENCODEV19/N4293-1_S5_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-S5-2x50mers-STAR2.5.3a-GENCODEV19/N4293-1_S5_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-N4293-rep1-S5.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-S5-2x50mers-STAR2.5.3a-GENCODEV19/N4293-2_S6_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-S5-2x50mers-STAR2.5.3a-GENCODEV19/N4293-2_S6_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-S5-2x50mers-STAR2.5.3a-GENCODEV19/N4293-2_S6_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep1-S5-2x50mers-STAR2.5.3a-GENCODEV19/N4293-2_S6_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-N4293-rep1-S5.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2-2x50mers-STAR2.5.3a-GENCODEV19/N4293-2_JT_CTCFvalidationRNAseq_170303_S2_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2-2x50mers-STAR2.5.3a-GENCODEV19/N4293-2_JT_CTCFvalidationRNAseq_170303_S2_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2-2x50mers-STAR2.5.3a-GENCODEV19/N4293-2_JT_CTCFvalidationRNAseq_170303_S2_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2-2x50mers-STAR2.5.3a-GENCODEV19/N4293-2_JT_CTCFvalidationRNAseq_170303_S2_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-N4293-rep2-JT_CTCFvalidationRNAseq_170303_S2.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3-2x50mers-STAR2.5.3a-GENCODEV19/N4371-1_JT_CTCFvalidationRNAseq_170303_S3_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3-2x50mers-STAR2.5.3a-GENCODEV19/N4371-1_JT_CTCFvalidationRNAseq_170303_S3_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3-2x50mers-STAR2.5.3a-GENCODEV19/N4371-1_JT_CTCFvalidationRNAseq_170303_S3_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3-2x50mers-STAR2.5.3a-GENCODEV19/N4371-1_JT_CTCFvalidationRNAseq_170303_S3_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-N4371-rep1-JT_CTCFvalidationRNAseq_170303_S3.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep1-S7-2x50mers-STAR2.5.3a-GENCODEV19/N4371-1_S7_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep1-S7-2x50mers-STAR2.5.3a-GENCODEV19/N4371-1_S7_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep1-S7-2x50mers-STAR2.5.3a-GENCODEV19/N4371-1_S7_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep1-S7-2x50mers-STAR2.5.3a-GENCODEV19/N4371-1_S7_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-N4371-rep1-S7.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4-2x50mers-STAR2.5.3a-GENCODEV19/N4371-2_JT_CTCFvalidationRNAseq_170303_S4_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4-2x50mers-STAR2.5.3a-GENCODEV19/N4371-2_JT_CTCFvalidationRNAseq_170303_S4_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4-2x50mers-STAR2.5.3a-GENCODEV19/N4371-2_JT_CTCFvalidationRNAseq_170303_S4_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4-2x50mers-STAR2.5.3a-GENCODEV19/N4371-2_JT_CTCFvalidationRNAseq_170303_S4_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-N4371-rep2-JT_CTCFvalidationRNAseq_170303_S4.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep2-S8-2x50mers-STAR2.5.3a-GENCODEV19/N4371-2_S8_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep2-S8-2x50mers-STAR2.5.3a-GENCODEV19/N4371-2_S8_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep2-S8-2x50mers-STAR2.5.3a-GENCODEV19/N4371-2_S8_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-N4371-rep2-S8-2x50mers-STAR2.5.3a-GENCODEV19/N4371-2_S8_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-07-14-N4371-rep2-S8.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12040-GH549_1_CTCFvalidationRNAseq_170812_S1-2x50mers-STAR2.5.3a-GENCODEV19/GH549_1_CTCFvalidationRNAseq_170812_S1_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12040-GH549_1_CTCFvalidationRNAseq_170812_S1-2x50mers-STAR2.5.3a-GENCODEV19/GH549_1_CTCFvalidationRNAseq_170812_S1_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12040-GH549_1_CTCFvalidationRNAseq_170812_S1-2x50mers-STAR2.5.3a-GENCODEV19/GH549_1_CTCFvalidationRNAseq_170812_S1_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12040-GH549_1_CTCFvalidationRNAseq_170812_S1-2x50mers-STAR2.5.3a-GENCODEV19/GH549_1_CTCFvalidationRNAseq_170812_S1_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-12040-GH549_1_CTCFvalidationRNAseq_170812_S1.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12040-GH549_2_CTCFvalidationRNAseq_170812_S2-2x50mers-STAR2.5.3a-GENCODEV19/GH549_2_CTCFvalidationRNAseq_170812_S2_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12040-GH549_2_CTCFvalidationRNAseq_170812_S2-2x50mers-STAR2.5.3a-GENCODEV19/GH549_2_CTCFvalidationRNAseq_170812_S2_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12040-GH549_2_CTCFvalidationRNAseq_170812_S2-2x50mers-STAR2.5.3a-GENCODEV19/GH549_2_CTCFvalidationRNAseq_170812_S2_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12040-GH549_2_CTCFvalidationRNAseq_170812_S2-2x50mers-STAR2.5.3a-GENCODEV19/GH549_2_CTCFvalidationRNAseq_170812_S2_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-12040-GH549_2_CTCFvalidationRNAseq_170812_S2.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12042-GH550_1_CTCFvalidationRNAseq_170812_S3-2x50mers-STAR2.5.3a-GENCODEV19/GH550_1_CTCFvalidationRNAseq_170812_S3_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12042-GH550_1_CTCFvalidationRNAseq_170812_S3-2x50mers-STAR2.5.3a-GENCODEV19/GH550_1_CTCFvalidationRNAseq_170812_S3_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12042-GH550_1_CTCFvalidationRNAseq_170812_S3-2x50mers-STAR2.5.3a-GENCODEV19/GH550_1_CTCFvalidationRNAseq_170812_S3_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12042-GH550_1_CTCFvalidationRNAseq_170812_S3-2x50mers-STAR2.5.3a-GENCODEV19/GH550_1_CTCFvalidationRNAseq_170812_S3_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-12042-GH550_1_CTCFvalidationRNAseq_170812_S3.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12042-GH550_2_CTCFvalidationRNAseq_170812_S4-2x50mers-STAR2.5.3a-GENCODEV19/GH550_2_CTCFvalidationRNAseq_170812_S4_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12042-GH550_2_CTCFvalidationRNAseq_170812_S4-2x50mers-STAR2.5.3a-GENCODEV19/GH550_2_CTCFvalidationRNAseq_170812_S4_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12042-GH550_2_CTCFvalidationRNAseq_170812_S4-2x50mers-STAR2.5.3a-GENCODEV19/GH550_2_CTCFvalidationRNAseq_170812_S4_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-12042-GH550_2_CTCFvalidationRNAseq_170812_S4-2x50mers-STAR2.5.3a-GENCODEV19/GH550_2_CTCFvalidationRNAseq_170812_S4_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-12042-GH550_2_CTCFvalidationRNAseq_170812_S4.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9-2x50mers-STAR2.5.3a-GENCODEV19/13004_1_CTCFvalidationRNAseq_170812_S9_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9-2x50mers-STAR2.5.3a-GENCODEV19/13004_1_CTCFvalidationRNAseq_170812_S9_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9-2x50mers-STAR2.5.3a-GENCODEV19/13004_1_CTCFvalidationRNAseq_170812_S9_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9-2x50mers-STAR2.5.3a-GENCODEV19/13004_1_CTCFvalidationRNAseq_170812_S9_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-13004_1_CTCFvalidationRNAseq_170812_S9.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10-2x50mers-STAR2.5.3a-GENCODEV19/13004_2_CTCFvalidationRNAseq_170812_S10_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10-2x50mers-STAR2.5.3a-GENCODEV19/13004_2_CTCFvalidationRNAseq_170812_S10_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10-2x50mers-STAR2.5.3a-GENCODEV19/13004_2_CTCFvalidationRNAseq_170812_S10_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10-2x50mers-STAR2.5.3a-GENCODEV19/13004_2_CTCFvalidationRNAseq_170812_S10_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-13004_2_CTCFvalidationRNAseq_170812_S10.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11-2x50mers-STAR2.5.3a-GENCODEV19/13006_1_CTCFvalidationRNAseq_170812_S11_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11-2x50mers-STAR2.5.3a-GENCODEV19/13006_1_CTCFvalidationRNAseq_170812_S11_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11-2x50mers-STAR2.5.3a-GENCODEV19/13006_1_CTCFvalidationRNAseq_170812_S11_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11-2x50mers-STAR2.5.3a-GENCODEV19/13006_1_CTCFvalidationRNAseq_170812_S11_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-13006_1_CTCFvalidationRNAseq_170812_S11.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12-2x50mers-STAR2.5.3a-GENCODEV19/13006_2_CTCFvalidationRNAseq_170812_S12_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12-2x50mers-STAR2.5.3a-GENCODEV19/13006_2_CTCFvalidationRNAseq_170812_S12_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12-2x50mers-STAR2.5.3a-GENCODEV19/13006_2_CTCFvalidationRNAseq_170812_S12_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12-2x50mers-STAR2.5.3a-GENCODEV19/13006_2_CTCFvalidationRNAseq_170812_S12_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-13006_2_CTCFvalidationRNAseq_170812_S12.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14376-GH551_1_CTCFvalidationRNAseq_170812_S5-2x50mers-STAR2.5.3a-GENCODEV19/GH551_1_CTCFvalidationRNAseq_170812_S5_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14376-GH551_1_CTCFvalidationRNAseq_170812_S5-2x50mers-STAR2.5.3a-GENCODEV19/GH551_1_CTCFvalidationRNAseq_170812_S5_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14376-GH551_1_CTCFvalidationRNAseq_170812_S5-2x50mers-STAR2.5.3a-GENCODEV19/GH551_1_CTCFvalidationRNAseq_170812_S5_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14376-GH551_1_CTCFvalidationRNAseq_170812_S5-2x50mers-STAR2.5.3a-GENCODEV19/GH551_1_CTCFvalidationRNAseq_170812_S5_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-14376-GH551_1_CTCFvalidationRNAseq_170812_S5.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14376-GH551_2_CTCFvalidationRNAseq_170812_S6-2x50mers-STAR2.5.3a-GENCODEV19/GH551_2_CTCFvalidationRNAseq_170812_S6_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14376-GH551_2_CTCFvalidationRNAseq_170812_S6-2x50mers-STAR2.5.3a-GENCODEV19/GH551_2_CTCFvalidationRNAseq_170812_S6_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14376-GH551_2_CTCFvalidationRNAseq_170812_S6-2x50mers-STAR2.5.3a-GENCODEV19/GH551_2_CTCFvalidationRNAseq_170812_S6_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14376-GH551_2_CTCFvalidationRNAseq_170812_S6-2x50mers-STAR2.5.3a-GENCODEV19/GH551_2_CTCFvalidationRNAseq_170812_S6_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-14376-GH551_2_CTCFvalidationRNAseq_170812_S6.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14377-GH552_1_CTCFvalidationRNAseq_170812_S7-2x50mers-STAR2.5.3a-GENCODEV19/GH552_1_CTCFvalidationRNAseq_170812_S7_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14377-GH552_1_CTCFvalidationRNAseq_170812_S7-2x50mers-STAR2.5.3a-GENCODEV19/GH552_1_CTCFvalidationRNAseq_170812_S7_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14377-GH552_1_CTCFvalidationRNAseq_170812_S7-2x50mers-STAR2.5.3a-GENCODEV19/GH552_1_CTCFvalidationRNAseq_170812_S7_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14377-GH552_1_CTCFvalidationRNAseq_170812_S7-2x50mers-STAR2.5.3a-GENCODEV19/GH552_1_CTCFvalidationRNAseq_170812_S7_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-14377-GH552_1_CTCFvalidationRNAseq_170812_S7.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14377-GH552_2_CTCFvalidationRNAseq_170812_S8-2x50mers-STAR2.5.3a-GENCODEV19/GH552_2_CTCFvalidationRNAseq_170812_S8_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14377-GH552_2_CTCFvalidationRNAseq_170812_S8-2x50mers-STAR2.5.3a-GENCODEV19/GH552_2_CTCFvalidationRNAseq_170812_S8_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14377-GH552_2_CTCFvalidationRNAseq_170812_S8-2x50mers-STAR2.5.3a-GENCODEV19/GH552_2_CTCFvalidationRNAseq_170812_S8_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-14377-GH552_2_CTCFvalidationRNAseq_170812_S8-2x50mers-STAR2.5.3a-GENCODEV19/GH552_2_CTCFvalidationRNAseq_170812_S8_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-14377-GH552_2_CTCFvalidationRNAseq_170812_S8.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13-2x50mers-STAR2.5.3a-GENCODEV19/N4293_1_CTCFvalidationRNAseq_170812_S13_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13-2x50mers-STAR2.5.3a-GENCODEV19/N4293_1_CTCFvalidationRNAseq_170812_S13_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13-2x50mers-STAR2.5.3a-GENCODEV19/N4293_1_CTCFvalidationRNAseq_170812_S13_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13-2x50mers-STAR2.5.3a-GENCODEV19/N4293_1_CTCFvalidationRNAseq_170812_S13_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-N4293_1_CTCFvalidationRNAseq_170812_S13.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14-2x50mers-STAR2.5.3a-GENCODEV19/N4293_2_CTCFvalidationRNAseq_170812_S14_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14-2x50mers-STAR2.5.3a-GENCODEV19/N4293_2_CTCFvalidationRNAseq_170812_S14_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14-2x50mers-STAR2.5.3a-GENCODEV19/N4293_2_CTCFvalidationRNAseq_170812_S14_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14-2x50mers-STAR2.5.3a-GENCODEV19/N4293_2_CTCFvalidationRNAseq_170812_S14_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-N4293_2_CTCFvalidationRNAseq_170812_S14.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15-2x50mers-STAR2.5.3a-GENCODEV19/N4871_1_CTCFvalidationRNAseq_170812_S15_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15-2x50mers-STAR2.5.3a-GENCODEV19/N4871_1_CTCFvalidationRNAseq_170812_S15_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15-2x50mers-STAR2.5.3a-GENCODEV19/N4871_1_CTCFvalidationRNAseq_170812_S15_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15-2x50mers-STAR2.5.3a-GENCODEV19/N4871_1_CTCFvalidationRNAseq_170812_S15_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-N4871_1_CTCFvalidationRNAseq_170812_S15.50mers
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16-2x50mers-STAR2.5.3a-GENCODEV19/N4871_2_CTCFvalidationRNAseq_170812_S16_L001_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16-2x50mers-STAR2.5.3a-GENCODEV19/N4871_2_CTCFvalidationRNAseq_170812_S16_L002_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16-2x50mers-STAR2.5.3a-GENCODEV19/N4871_2_CTCFvalidationRNAseq_170812_S16_L003_R1_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16-2x50mers-STAR2.5.3a-GENCODEV19/N4871_2_CTCFvalidationRNAseq_170812_S16_L004_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L001_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L002_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L003_R2_001.fastq.gz,/oak/stanford/groups/akundaje/marinovg/ENCODE4/CRISPR/datasets-RNA-seq/2017-07-14-13004-rep1-S1-2x50mers-STAR2.5.3a-GENCODEV19/13004-1_S1_L004_R2_001.fastq.gz -trim 50 50 -minReadLen 50 | python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited-reverse.py - 2017-08-14-N4871_2_CTCFvalidationRNAseq_170812_S16.50mers