python ~/code/SAMstats.py Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Col-0_GFP_low_blue_light_ChIPseq-GSM3092813.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.bam SAMstats-Col-0_GFP_low_blue_light_ChIPseq-GSM3092813 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.bam SAMstats-OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.bam SAMstats-OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_GFP_low_blue_light_ChIPseq-GSM3092813/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_TZP_GFP_low_blue_light_ChIPseq-GSM3092814/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes OX_ZFHD10_GFP_low_blue_light_ChIPseq-GSM3092815/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM