python ~/code/SAMstats.py Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam SAMstats-Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam SAMstats-Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_4_hour_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Col-0_3-day_etiolated_seedlings_no_ethylene_EIN3_ChIP-Seq_rep1/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM