Question: Better statergy for Gap Closing
1
gravatar for ramesh.8v
4.8 years ago by
ramesh.8v200
United States
ramesh.8v200 wrote:

Hi Guys,

Couple of months back, I sequenced (MiSeq) few BACs and assembled (Paired-end reads) using SOAPdenovo, but my assembly was fallen into many scaffolds. Now, I got reference genome and trying to pull out my interested region (about 3.2 Mb). 

Here is my first approach:

I mapped paired-end reads to the reference genome and parsed out the scaffolds, those got mapped. Still, 3.2 Mb of my region is spreaded into 26 scaffolds. I believe, I can able to close these gaps with my Paired-end data. I also got genome of other three very related species to aid me in gap closing.

Now, my question is, what would be the best approach to close gaps?

Many thanks in advance

Ramesh

gapclosing ngs assembly • 1.7k views
ADD COMMENTlink modified 4.8 years ago by 5heikki8.6k • written 4.8 years ago by ramesh.8v200

Have you tried something like gapfiller ? http://genomebiology.com/2012/13/6/R56

ADD REPLYlink written 4.8 years ago by MiguelMorard20
1
gravatar for 5heikki
4.8 years ago by
5heikki8.6k
Finland
5heikki8.6k wrote:

I've had moderate success closing gaps of metagenomic bins with PRICE (paper).

ADD COMMENTlink written 4.8 years ago by 5heikki8.6k
0
gravatar for alexcd201403
4.8 years ago by
alexcd20140330
USA
alexcd20140330 wrote:

There are quite a lot you can find methods in paper: National Integrated Strategy for Closing the Gap in Indigenous Disadvantage, and some others Strategies for Closing the Achievement Gaps, try to search these methods I referred. 

ADD COMMENTlink written 4.8 years ago by alexcd20140330

National Integrated Strategy for Closing the Gap in Indigenous Disadvantage:

"This Strategy acknowledges the importance of Indigenous culture, and engagement and positive relationships with Indigenous Australians. It discusses the contribution of the current COAG reform initiatives to meeting the targets and also the frameworks for accountability and performance reporting. Finally, it discusses directions for future work."

Strategies for Closing the Achievement Gaps:

"After you examine the data for your school or district, you can begin to identify the best strategies for you to use for closing the gaps. As you discuss these strategies, keep in mind (a) which strategies are already in place; (b) what resources are needed to implement new strategies; and (c) what new actions are needed. Below are strategies you may consider using."

 

Please don't just google the the thread title and post the first few hits...

ADD REPLYlink written 4.8 years ago by pld4.8k

Yes, I would request author to please take off the answer.

ADD REPLYlink written 4.8 years ago by ramesh.8v200
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