python ~/code/SAMstats.py FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-FUL-GFP_in_ful-1_replicate_1-GSM2098200.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.bam SAMstats-FUL-GFP_in_ful-1_replicate_1-GSM2098200 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-FUL-GFP_in_ful-1_replicate_2-GSM2098201.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.bam SAMstats-FUL-GFP_in_ful-1_replicate_2-GSM2098201 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Input_DNA_of_replicate_1_GFF-1-GSM2098202.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.bam SAMstats-Input_DNA_of_replicate_1_GFF-1-GSM2098202 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Input_DNA_of_replicate_2_GBY-1-GSM2098203.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.bam SAMstats-Input_DNA_of_replicate_2_GBY-1-GSM2098203 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_1-GSM2098200/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes FUL-GFP_in_ful-1_replicate_2-GSM2098201/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_1_GFF-1-GSM2098202/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Input_DNA_of_replicate_2_GBY-1-GSM2098203/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM