Break the assembled genome by error-some regions !
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Can you add additional clarification on what you are trying to do? Is the genome assembled from the same reads you are using? If it was then how did you do the assembly? What program did you use?
What do you mean by this bit?
Falcon were used to assemble the genome. After mapping, I notice such cases https://dazzlerblog.files.wordpress.com/2017/04/screen-shot-2017-04-18-at-9-54-01-am.png
I wanted to break the genome by those "error-some" regions (by middle of X and Y in the figure) and re-scaffold them. How to break the assembled genome my such regions ?
So the non-white lines in the image are sequences that should not be there (or you are not interested in)? Is that leftover adapter contamination that was somehow incorporated in the assembly?
Hey BioGeek,
Have you carried out any filtering, trimming or adapter cleaning on the raw ONT reads? It is recommended to do some basic cleaning on the reads before aligning/assembling them. You could use tools like nanofilt or Porechop for ONT reads QC.