python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.gtf G2-1_fix_180918.s180918_S1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig 1000 coverage-G2-1_fix_180918.s180918_S1.Schizosaccharomyces_pombe.ASM294v2.20 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.gtf G2-2_fix_180918.s180918_S2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig 1000 coverage-G2-2_fix_180918.s180918_S2.Schizosaccharomyces_pombe.ASM294v2.20 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.gtf G2-3_fix_180918.s180918_S3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig 1000 coverage-G2-3_fix_180918.s180918_S3.Schizosaccharomyces_pombe.ASM294v2.20 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.gtf G2-4_fix_180918.s180918_S4-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig 1000 coverage-G2-4_fix_180918.s180918_S4.Schizosaccharomyces_pombe.ASM294v2.20 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.gtf input_fix_180918.s180918_SA-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig 1000 coverage-input_fix_180918.s180918_SA.Schizosaccharomyces_pombe.ASM294v2.20 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.2019-02-06-PomBase.fixed.gtf input_live_180918.s180918_SB-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig 1000 coverage-input_live_180918.s180918_SB.Schizosaccharomyces_pombe.ASM294v2.20 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.gtf G2-1_fix_180918.s180918_S1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig 1000 coverage-G2-1_fix_180918.s180918_S1.sacCer3 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.gtf G2-2_fix_180918.s180918_S2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig 1000 coverage-G2-2_fix_180918.s180918_S2.sacCer3 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.gtf G2-3_fix_180918.s180918_S3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig 1000 coverage-G2-3_fix_180918.s180918_S3.sacCer3 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.gtf G2-4_fix_180918.s180918_S4-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig 1000 coverage-G2-4_fix_180918.s180918_S4.sacCer3 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.gtf input_fix_180918.s180918_SA-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig 1000 coverage-input_fix_180918.s180918_SA.sacCer3 -normalize -singlemodelgenes &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gene_coverage_wig_gtf.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated.gtf input_live_180918.s180918_SB-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig 1000 coverage-input_live_180918.s180918_SB.sacCer3 -normalize -singlemodelgenes &
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-1_fix_180918.s180918_S1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes G2-1_fix_180918.s180918_S1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-2_fix_180918.s180918_S2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes G2-2_fix_180918.s180918_S2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-3_fix_180918.s180918_S3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes G2-3_fix_180918.s180918_S3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-4_fix_180918.s180918_S4-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes G2-4_fix_180918.s180918_S4-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig input_fix_180918.s180918_SA-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes input_fix_180918.s180918_SA-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig input_live_180918.s180918_SB-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes input_live_180918.s180918_SB-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-1_fix_180918.s180918_S1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes G2-1_fix_180918.s180918_S1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-2_fix_180918.s180918_S2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes G2-2_fix_180918.s180918_S2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-3_fix_180918.s180918_S3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes G2-3_fix_180918.s180918_S3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-4_fix_180918.s180918_S4-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes G2-4_fix_180918.s180918_S4-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig input_fix_180918.s180918_SA-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes input_fix_180918.s180918_SA-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig input_live_180918.s180918_SB-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes input_live_180918.s180918_SB-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-1_fix_180918.s180918_S1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes G2-1_fix_180918.s180918_S1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-2_fix_180918.s180918_S2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes G2-2_fix_180918.s180918_S2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-3_fix_180918.s180918_S3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes G2-3_fix_180918.s180918_S3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-4_fix_180918.s180918_S4-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes G2-4_fix_180918.s180918_S4-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig input_fix_180918.s180918_SA-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes input_fix_180918.s180918_SA-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig input_live_180918.s180918_SB-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/sacCer3.chrom.sizes input_live_180918.s180918_SB-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.sacCer3.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-1_fix_180918.s180918_S1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes G2-1_fix_180918.s180918_S1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-2_fix_180918.s180918_S2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes G2-2_fix_180918.s180918_S2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-3_fix_180918.s180918_S3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes G2-3_fix_180918.s180918_S3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig G2-4_fix_180918.s180918_S4-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes G2-4_fix_180918.s180918_S4-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig input_fix_180918.s180918_SA-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes input_fix_180918.s180918_SA-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.bigWig
/oak/stanford/groups/akundaje/marinovg/programs/UCSC-utils-2017-07-13/wigToBigWig input_live_180918.s180918_SB-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.wig /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/combined_indexes/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes input_live_180918.s180918_SB-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.Schizosaccharomyces_pombe.ASM294v2.20.unique.bigWig