python ~/code/SAMstats.py SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.bam SAMstats-SEP3_ChIPSeq_wt_1-GSM364939 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-SEP3_ChIPSeq_wt_1-GSM364939.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.bam SAMstats-SEP3_ChIPSeq_wt_2-GSM364940 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-SEP3_ChIPSeq_wt_2-GSM364940.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.bam SAMstats-SEP3_ChIPSeq_sep3_3-GSM364941 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-SEP3_ChIPSeq_sep3_3-GSM364941.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.bam SAMstats-SEP3_ChIPSeq_wt_3-GSM364942 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-SEP3_ChIPSeq_wt_3-GSM364942.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.bam SAMstats-SEP3_ChIPSeq_ag_3-GSM364943 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-SEP3_ChIPSeq_ag_3-GSM364943.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_1-GSM364939/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_2-GSM364940/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_sep3_3-GSM364941/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_wt_3-GSM364942/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3_ChIPSeq_ag_3-GSM364943/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM