i have merged uniquely aligned peaks files for each replicates of sample into one .bed file per sample then generate file cellmarkfiletable_hg38.txt cellmarkfiletable_hg38.txt
<h5>after this i have used to binazriedbed file via using this command:</h5>java -mx4000M -jar /home/data/iqra/H4K16ac/H9/bamtobed/merged_peaks/ChromHMM/ChromHMM-master/ChromHMM.jar BinarizeBed /home/data/iqra/H4K16ac/H9/bamtobed/hg38.chrom.sizes /home/data/iqra/H4K16ac/H9/bamtobed/merged_peaks /home/data/iqra/H4K16ac/H9/bamtobed/chromHmm/cellmarkfiletable_hg38.txt /home/data/iqra/H4K16ac/H9/bamtobed/chromHmm/outputsignaldir
then used
$java -mx8000M -jar /home/data/iqra/H4K16ac/H9/bamtobed/merged_peaks/ChromHMM/ChromHMM-master/ChromHMM.jar LearnModel -p 4 -l /home/data/iqra/H4K16ac/H9/bamtobed/hg38.chrom.sizes /home/data/iqra/H4K16ac/H9/bamtobed/chromHmm/outputsignaldir /home/data/iqra/H4K16ac/H9/bamtobed/chromHmm/chromatin_states 5 hg38
im trying to reanalyzed paper data and generated a reference plot as they have generated
emissions_5.txt a, Bar chart showing the percentage distribution (y axis) of histone PTMs CUT&Tag peaks across ChromHMM chromatin features. Low signal (Lo), transcription (Txn)
could you please guide me how i can annotate these states. while using this i got an error (bioinformatics) iqra@bio-Super-Server:~/H4K16ac/H9/bamtobed/merged_peaks$ java -mx8000M -jar /home/data/iqra/H4K16ac/H9/bamtobed/merged_peaks/ChromHMM/ChromHMM-master/ChromHMM.jar LearnModel \
-p 0 -l /home/data/iqra/H4K16ac/H9/bamtobed/hg38.chrom.sizes -init RANDOM /home/data/iqra/H4K16ac/H9/bamtobed/chromHmm/outputsignaldir /home/data/iqra/H4K16ac/H9/bamtobed/chromHmm/chromatin_states 10 hg38 usage: LearnModel [-b binsize][-color r,g,b][-d convergedelta][-e loadsmoothemission][-f inputfilelist][-gzip][-h informationsmooth][-holdcolumnorder][-holdroworder][-i outfileID][-init information|random|load][-l chromosomelengthfile][-lowmem][-m modelinitialfile][-many][-n numseq][-noautoopen][-nobed][-nobrowser][-nobrowserheader][-noenrich][-noimage][-nopseudolast][-p maxprocessors][-pseudo][-printposterior][-printstatebyline][-r maxiterations][-s seed][-scalebeta][-splitrows][-stateordering emission|transition][-t loadsmoothtransition][-u coorddir][-v anchorfiledir][-x maxseconds][-z zerotransitionpower] inputdir outputdir numstates assembly (bioinformatics) iqra@bio-Super-Server:~/H4K16ac/H9/bamtobed/merged_peaks$
