python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py HL_1-GSM3188718-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-HL_1-GSM3188718-STAR -bam  /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py HL_2-GSM3188719-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-HL_2-GSM3188719-STAR -bam  /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py HL_3-GSM3188720-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-HL_3-GSM3188720-STAR -bam  /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LL_1-GSM3188715-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-LL_1-GSM3188715-STAR -bam  /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LL_2-GSM3188716-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-LL_2-GSM3188716-STAR -bam  /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py LL_3-GSM3188717-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-LL_3-GSM3188717-STAR -bam  /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py VL_1-GSM3188712-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-VL_1-GSM3188712-STAR -bam  /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py VL_2-GSM3188713-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-VL_2-GSM3188713-STAR -bam  /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py VL_3-GSM3188714-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-VL_3-GSM3188714-STAR -bam  /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes samtools
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigna1_filtered_genes.gtf HL_1-GSM3188718-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes sam_reads_in_genes-HL_1-GSM3188718 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigna1_filtered_genes.gtf HL_2-GSM3188719-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes sam_reads_in_genes-HL_2-GSM3188719 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigna1_filtered_genes.gtf HL_3-GSM3188720-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes sam_reads_in_genes-HL_3-GSM3188720 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigna1_filtered_genes.gtf LL_1-GSM3188715-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes sam_reads_in_genes-LL_1-GSM3188715 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigna1_filtered_genes.gtf LL_2-GSM3188716-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes sam_reads_in_genes-LL_2-GSM3188716 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigna1_filtered_genes.gtf LL_3-GSM3188717-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes sam_reads_in_genes-LL_3-GSM3188717 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigna1_filtered_genes.gtf VL_1-GSM3188712-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes sam_reads_in_genes-VL_1-GSM3188712 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigna1_filtered_genes.gtf VL_2-GSM3188713-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes sam_reads_in_genes-VL_2-GSM3188713 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigna1_filtered_genes.gtf VL_3-GSM3188714-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes sam_reads_in_genes-VL_3-GSM3188714 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- HL_1-GSM3188718-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes HL_1-GSM3188718-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.wig -RPM -notitle -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- HL_2-GSM3188719-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes HL_2-GSM3188719-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.wig -RPM -notitle -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- HL_3-GSM3188720-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes HL_3-GSM3188720-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.wig -RPM -notitle -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LL_1-GSM3188715-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes LL_1-GSM3188715-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.wig -RPM -notitle -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LL_2-GSM3188716-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes LL_2-GSM3188716-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.wig -RPM -notitle -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- LL_3-GSM3188717-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes LL_3-GSM3188717-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.wig -RPM -notitle -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- VL_1-GSM3188712-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes VL_1-GSM3188712-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.wig -RPM -notitle -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- VL_2-GSM3188713-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes VL_2-GSM3188713-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.wig -RPM -notitle -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- VL_3-GSM3188714-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes VL_3-GSM3188714-STAR/STAR-2.5.3a-Aligned.sortedByCoord.out.wig -RPM -notitle -nomulti