export PATH=~/programs/samtools-0.1.19/:$PATH; export PATH=$PATH:~/programs/bowtie-0.12.9/; export PATH=$PATH:~/programs/tophat-2.0.8.Linux_x86_64/; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 20 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -o C2-1_Diff_rep1-GSM3028917-2x75mers-TopHat-2.0.8-GENCODE_V25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male C2-1_Diff_rep1-GSM3028917/SRR6798424_1.fastq.gz C2-1_Diff_rep1-GSM3028917/SRR6798424_2.fastq.gz
export PATH=~/programs/samtools-0.1.19/:$PATH; export PATH=$PATH:~/programs/bowtie-0.12.9/; export PATH=$PATH:~/programs/tophat-2.0.8.Linux_x86_64/; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 20 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -o C2-1_Undiff_rep1-GSM3028913-2x75mers-TopHat-2.0.8-GENCODE_V25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male C2-1_Undiff_rep1-GSM3028913/SRR6798420_1.fastq.gz C2-1_Undiff_rep1-GSM3028913/SRR6798420_2.fastq.gz
export PATH=~/programs/samtools-0.1.19/:$PATH; export PATH=$PATH:~/programs/bowtie-0.12.9/; export PATH=$PATH:~/programs/tophat-2.0.8.Linux_x86_64/; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 20 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -o C2-2_Diff_rep1-GSM3028918-2x75mers-TopHat-2.0.8-GENCODE_V25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male C2-2_Diff_rep1-GSM3028918/SRR6798425_1.fastq.gz C2-2_Diff_rep1-GSM3028918/SRR6798425_2.fastq.gz
export PATH=~/programs/samtools-0.1.19/:$PATH; export PATH=$PATH:~/programs/bowtie-0.12.9/; export PATH=$PATH:~/programs/tophat-2.0.8.Linux_x86_64/; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 20 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -o C2-2_Undiff_rep1-GSM3028914-2x75mers-TopHat-2.0.8-GENCODE_V25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male C2-2_Undiff_rep1-GSM3028914/SRR6798421_1.fastq.gz C2-2_Undiff_rep1-GSM3028914/SRR6798421_2.fastq.gz
export PATH=~/programs/samtools-0.1.19/:$PATH; export PATH=$PATH:~/programs/bowtie-0.12.9/; export PATH=$PATH:~/programs/tophat-2.0.8.Linux_x86_64/; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 20 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -o R2-1_Diff_rep1-GSM3028919-2x75mers-TopHat-2.0.8-GENCODE_V25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male R2-1_Diff_rep1-GSM3028919/SRR6798426_1.fastq.gz R2-1_Diff_rep1-GSM3028919/SRR6798426_2.fastq.gz
export PATH=~/programs/samtools-0.1.19/:$PATH; export PATH=$PATH:~/programs/bowtie-0.12.9/; export PATH=$PATH:~/programs/tophat-2.0.8.Linux_x86_64/; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 20 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -o R2-1_Undiff_rep1-GSM3028915-2x75mers-TopHat-2.0.8-GENCODE_V25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male R2-1_Undiff_rep1-GSM3028915/SRR6798422_1.fastq.gz R2-1_Undiff_rep1-GSM3028915/SRR6798422_2.fastq.gz
export PATH=~/programs/samtools-0.1.19/:$PATH; export PATH=$PATH:~/programs/bowtie-0.12.9/; export PATH=$PATH:~/programs/tophat-2.0.8.Linux_x86_64/; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 20 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -o R2-2_Diff_rep1-GSM3028920-2x75mers-TopHat-2.0.8-GENCODE_V25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male R2-2_Diff_rep1-GSM3028920/SRR6798427_1.fastq.gz R2-2_Diff_rep1-GSM3028920/SRR6798427_2.fastq.gz
export PATH=~/programs/samtools-0.1.19/:$PATH; export PATH=$PATH:~/programs/bowtie-0.12.9/; export PATH=$PATH:~/programs/tophat-2.0.8.Linux_x86_64/; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 20 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -o R2-2_Undiff_rep1-GSM3028916-2x75mers-TopHat-2.0.8-GENCODE_V25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male R2-2_Undiff_rep1-GSM3028916/SRR6798423_1.fastq.gz R2-2_Undiff_rep1-GSM3028916/SRR6798423_2.fastq.gz
export PATH=~/programs/samtools-0.1.19/:$PATH; export PATH=$PATH:~/programs/bowtie-0.12.9/; export PATH=$PATH:~/programs/tophat-2.0.8.Linux_x86_64/;