How To Obtain The Exact Breakpoint Location Using Local Aseembled Contigs

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12.9 years ago

Junfeng ▴ 330

Hi, I have used the BreakDancer (http://breakdancer.sourceforge.net/) to call structure variants and then used Tigra_SV to perform the assembly of structural variants. Now I have obtained the local assembly from Tigra_SV (http://genome.wustl.edu/software/tigra_sv), but I did not know how to remove false positives of SV and precisely define breakpoint using this result. I am new to next generation sequencing so any help would be appreciated. Thanks.

next-gen sequencing structural local • 3.3k views

ADD COMMENT • link updated 12.8 years ago by Lars Juhl Jensen 11k • written 12.9 years ago by Junfeng ▴ 330

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@Junfeng -- i am at the same stage as you are. I have the breakdancer output and done the tigra_sv assembly but am wondering how to precisely define breakpoint using the output. were you able to resolve your query? Any comment is highly appreciated...!Thanks

ADD REPLY • link 12.8 years ago by Hmm ▴ 500

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You can try CREST http://www.nature.com/nmeth/journal/v8/n8/full/nmeth.1628.html.

ADD REPLY • link 12.7 years ago by Junfeng ▴ 330

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