#p300-lost-maintained
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/lost-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_lost_p300.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee-r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/maintained-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_maintained_p300.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-lost-peaks-promoters.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_lost_p300_promoters.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-maintained-peaks-promoters.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_maintained_p300_promoters.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-lost-peaks-enhancers.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_lost_p300_enhancers.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-maintained-peaks-enhancers.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_maintained_p300_enhancers.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r

#p300-unbiased-up
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/unbiased-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_unbiased_p300.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/up-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_up_p300.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-unbiased-peaks-promoters.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_unbiased_p300_promoters.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-up-peaks-promoters.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_up_p300_promoters.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-unbiased-peaks-enhancers.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_unbiased_p300_enhancers.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-up-peaks-enhancers.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_up_p300_enhancers.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r

#p300-unbiased-up-1kb-window
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/unbiased-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_unbiased_p300_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r  -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/up-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_up_p300_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-unbiased-peaks-promoters.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_unbiased_p300_promoters_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-up-peaks-promoters.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_up_p300_promoters_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-unbiased-peaks-enhancers.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_unbiased_p300_enhancers_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-up-peaks-enhancers.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_up_p300_enhancers_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500

#p300-lost-maintained-1kb-window
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/lost-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_lost_p300_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/maintained-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_maintained_p300_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-lost-peaks-promoters.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_lost_p300_promoters_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-maintained-peaks-promoters.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_maintained_p300_promoters_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-lost-peaks-enhancers.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_lost_p300_enhancers_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-maintained-peaks-enhancers.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_p300a-ni_H3K4me1a-ni_on_maintained_p300_enhancers_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,009fee,009fee,009fee,009fee -r -e 500

#p300-lost-maintained-H3K9ac
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/lost-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_lost_p300.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/maintained-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_maintained_p300.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-lost-peaks-promoters -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_lost_p300_promoters.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-maintained-peaks-promoters.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_maintained_p300_promoters.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-lost-peaks-enhancers -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_lost_p300_enhancers.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-maintained-peaks-enhancers.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_maintained_p300_enhancers.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r

#p300-lost-maintained-H3K9ac-1kb-window
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/lost-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_lost_p300_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/maintained-peaks-p300.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_maintained_p300_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r -e 500

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-lost-peaks-promoters -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_lost_p300_promoters_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-maintained-peaks-promoters.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_maintained_p300_promoters_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r -e 500

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-lost-peaks-enhancers -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_lost_p300_enhancers_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/p300-maintained-peaks-enhancers.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/p300-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/p300-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_p300a-ni_H3K9aca-ni_on_maintained_p300_enhancers_1kb-window.png -C kmeans -k 5 -c cd9d15,cd9d15,cd9d15,cd9d15,f800fe,f800fe,f800fe,f800fe -r -e 500

#H3K4me3
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/lost-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_H3K4me3a-ni_H3K4me1a-ni_on_lost_H3K4me3.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,009fee,009fee,009fee,009fee -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/maintained-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_H3K4me3a-ni_H3K4me1a-ni_on_maintained_H3K4me3.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,009fee,009fee,009fee,009fee -r

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/lost-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_H3K4me3a-ni_H3K9aca-ni_on_lost_H3K4me3.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,f800fe,f800fe,f800fe,f800fe -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/maintained-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_H3K4me3a-ni_H3K9aca-ni_on_maintained_H3K4me3.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,f800fe,f800fe,f800fe,f800fe -r

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/unbiased-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_H3K4me3a-ni_H3K4me1a-ni_on_unbiased_H3K4me3.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,009fee,009fee,009fee,009fee -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/up-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_H3K4me3a-ni_H3K4me1a-ni_on_up_H3K4me3.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,009fee,009fee,009fee,009fee -r

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/unbiased-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_H3K4me3a-ni_H3K9aca-ni_on_unbiased_H3K4me3.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,f800fe,f800fe,f800fe,f800fe -r
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/up-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_H3K4me3a-ni_H3K9aca-ni_on_up_H3K4me3.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,f800fe,f800fe,f800fe,f800fe -r

#H3K4me3-1kb-window
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/lost-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_H3K4me3a-ni_H3K4me1a-ni_on_lost_H3K4me3_1kb-window.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,009fee,009fee,009fee,009fee -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/maintained-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_H3K4me3a-ni_H3K4me1a-ni_on_maintained_H3K4me3_1kb-window.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,009fee,009fee,009fee,009fee -r -e 500

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/lost-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_H3K4me3a-ni_H3K9aca-ni_on_lost_H3K4me3_1kb-window.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,f800fe,f800fe,f800fe,f800fe -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/maintained-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_H3K4me3a-ni_H3K9aca-ni_on_maintained_H3K4me3_1kb-window.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,f800fe,f800fe,f800fe,f800fe -r -e 500

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/unbiased-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_H3K4me3a-ni_H3K4me1a-ni_on_unbiased_H3K4me3_1kb-window.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,009fee,009fee,009fee,009fee -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/up-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me1-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K4me1_st11a.bam -o Heatmap_H3K4me3a-ni_H3K4me1a-ni_on_up_H3K4me3_1kb-window.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,009fee,009fee,009fee,009fee -r -e 500

fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/unbiased-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_H3K4me3a-ni_H3K9aca-ni_on_unbiased_H3K4me3_1kb-window.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,f800fe,f800fe,f800fe,f800fe -r -e 500
fluff heatmap -f /home/saartje/data/xt9.0/peaks/aam_final/BED/up-peaks-H3K4me3.bed -d /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11ni-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep1/H3K4me3-st11a-rep1.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K4me3-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-rep2/H3K9ac-st11a.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11ni.bam /home/saartje/data/xt9.0/bam/amanitin-K9ac-K4me1/H3K9ac_st11a.bam -o Heatmap_H3K4me3a-ni_H3K9aca-ni_on_up_H3K4me3_1kb-window.png -C kmeans -k 5 -c 41AB5D,41AB5D,41AB5D,41AB5D,f800fe,f800fe,f800fe,f800fe -r -e 500