Optimize step input file

[YuChrming]

Dear Professor， I have a small wonder , when I execute "Optimize" and "plot" steps, I have tried the sample.clean.bam after "Filtering SAM file" and prunning.bam after "Prune" . I find cleaner hic-sign in prunning.bam output but overall graphics of both consistent. So which one should I use?

Thanks very much!

Optimize
ordering and orientation for each group.

Usage:  

allhic extract sample.clean.bam draft.asm.fasta --RE AAGCTT  
allhic optimize group1.txt sample.clean.clm
allhic optimize group2.txt sample.clean.clm
...
allhic optimize group16.txt sample.clean.clm

Parameters:  

allhic extract  
    Input files:  
        bam file and contig-level assembly
    Options:
        --RE value  Restriction site pattern (default: "GATC")

plot
We will generate the chromatin contact matrix to evaluate genome scaffolding

Usage:  

ALLHiC_plot sample.clean.bam groups.agp chrn.list 500k pdf