python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.5p.wig -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.5p.wig -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.5p.wig -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.5p.wig -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.minus.5p.wig -stranded - -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.minus.5p.wig -stranded - -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.minus.5p.wig -stranded - -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.minus.5p.wig -stranded - -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.counts.plus.5p.wig -stranded + -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.RPM.plus.5p.wig -stranded + -RPM -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.RPM.plus.5p.wig -stranded + -RPM -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.A-SRX9295974-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Bz.B-SRX9295975-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.A-SRX9295976-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes ME49.Tz.B-SRX9295977-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.A-SRX9295978-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py --- RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/Toxoplasma_gondii.ToxoDB-7.1.20.chrom.sizes RH.Tz.B-SRX9295979-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.unique.counts.plus.5p.wig -stranded + -nomulti -notitle -end1only