Re: [Breakdancer-help] Help with breakdancer

[Ken C. <kch...@gm...>]

I would analyze these libraries individually (provided each having sufficient coverage) and look for inversion breakpoints that are consistently detected.
Longer insert size would be more helpful to detect inversion breakpoints in repeats.
You would also try Delly.

On Nov 19, 2014, at 7:56 AM, Pallavi Chauhan <pal...@bi...> wrote:

> 
> From: Pallavi Chauhan
> Sent: Wednesday, November 19, 2014 2:55 PM
> To: he...@li...
> Cc: kc...@wu...
> Subject: Help with breakdancer
> 
> Hi,
> My name is Pallavi and i am working as a post doc at Lund University Lund Sweden.
> I have started using Breakdancer to find inversions in the assembled genome. I have certain queries regarding running Breakdancer. Before i state my queries i would like to give a brief introduction about my work.
> I have assembled a genome using illumina paired -end 170bp, 500bp, 2000bp and 5000bp insert size libraries. Now i want to find inversion within the genome, since we don't have any closely related reference genome, i was thinking to map the libraries against the assembled genome to find the inversions.
> Now my queries are-
> 
> 1) Whether mapping the libraries back to the assembled genome would give correct information about the inversions?.
> 2) Which library among four would you think can help to find the accurate inversions?
> 3) Can to suggest some other equally good tools to validate the inversion results?.
> 
> 
> Eagerly waiting for your reply
> Thanking you
> 
> Best Regards
> 
> 
> Pallavi
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