python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.bam SAMstats-Population_STARR-seq_Input_Plasmid_Library-GSM2058394 -paired -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.bam SAMstats-Population_STARR-seq_Rep1-GSM2058391 -paired -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.bam SAMstats-Population_STARR-seq_Rep2-GSM2058392 -paired -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.bam SAMstats-Population_STARR-seq_Rep3-GSM2058393 -paired -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.InsertLength
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.InsertLength
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.InsertLength
python /oak/stanford/groups/akundaje/marinovg/code/PEInsertDistFromBAM.py Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.InsertLength
python /oak/stanford/groups/akundaje/marinovg/code/STARR-seq/fragmentCount.py Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.bam,Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.bam,Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.bam Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq.fragment_counts -singleFieldCoords
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.wig -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.wig -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.wig -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.wig -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.plus.wig -stranded + -fragments first-read-strand -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.plus.wig -stranded + -fragments first-read-strand -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.plus.wig -stranded + -fragments first-read-strand -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.plus.wig -stranded + -fragments first-read-strand -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Input_Plasmid_Library-GSM2058394/alignments.2x36mers.unique.minus.wig -stranded - -fragments first-read-strand -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep1-GSM2058391/alignments.2x36mers.unique.minus.wig -stranded - -fragments first-read-strand -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep2-GSM2058392/alignments.2x36mers.unique.minus.wig -stranded - -fragments first-read-strand -notitle -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes Population_STARR-seq_Rep3-GSM2058393/alignments.2x36mers.unique.minus.wig -stranded - -fragments first-read-strand -notitle -uniqueBAM