source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --passeq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/PAS-seq/primary_keratinocyte-d00.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d0.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d00.PAS-seq.b1.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d00.PAS-seq.b1.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --passeq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/PAS-seq/primary_keratinocyte-d00.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d0.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d00.PAS-seq.b2.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d00.PAS-seq.b2.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --passeq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/PAS-seq/primary_keratinocyte-d30.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d3.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d30.PAS-seq.b1.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d30.PAS-seq.b1.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --passeq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/PAS-seq/primary_keratinocyte-d30.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d3.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d30.PAS-seq.b2.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d30.PAS-seq.b2.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --passeq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/PAS-seq/primary_keratinocyte-d60.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d6.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d60.PAS-seq.b1.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d60.PAS-seq.b1.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --passeq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/PAS-seq/primary_keratinocyte-d60.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d6.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d60.PAS-seq.b2.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d60.PAS-seq.b2.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --rampage-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RAMPAGE/primary_keratinocyte-d00.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d0.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d00.RAMPAGE.b1.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d00.RAMPAGE.b1.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --rampage-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RAMPAGE/primary_keratinocyte-d00.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d0.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d00.RAMPAGE.b2.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d00.RAMPAGE.b2.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --rampage-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RAMPAGE/primary_keratinocyte-d30.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d3.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d30.RAMPAGE.b1.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d30.RAMPAGE.b1.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --rampage-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RAMPAGE/primary_keratinocyte-d30.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d3.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d30.RAMPAGE.b2.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d30.RAMPAGE.b2.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --rampage-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RAMPAGE/primary_keratinocyte-d60.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d6.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d60.RAMPAGE.b1.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d60.RAMPAGE.b1.bed
source activate grit-2.0.5; /oak/stanford/groups/akundaje/marinovg/programs/GRIT-2.0.5/bin/call_peaks --rampage-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RAMPAGE/primary_keratinocyte-d60.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --rnaseq-reads /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d6.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam --threads 8 --reference /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf --outfname GRIT-2.0.5.call_peaks.primary_keratinocyte-d60.RAMPAGE.b2.gff  --outfname-type gff --bed-peaks-ofname GRIT-2.0.5.call_peaks.primary_keratinocyte-d60.RAMPAGE.b2.bed