Question: Removed contigs and genes from assembly by HaploMerger
0
gravatar for Mehmet
4.0 years ago by
Mehmet470
Japan
Mehmet470 wrote:

I used HaploMerger, now I want to see which contigs and genes were removed from assembly by HaploMerger. How can I do that?

Thanks

ADD COMMENTlink modified 3.7 years ago by mapleforest10 • written 4.0 years ago by Mehmet470
0
gravatar for thackl
3.8 years ago by
thackl2.6k
MIT
thackl2.6k wrote:

One way to go would by alignment of the old and new assembly. A very fast way is probably bwa mem - viewing the resulting BAM file in IGV or similar is also straight forward. A more sophisticated way would be using mummer/nucmer, the results can be visualized as dotplots as well.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by thackl2.6k
0
gravatar for mapleforest
3.7 years ago by
mapleforest10
mapleforest10 wrote:

You can try HaploMerger2, the newly-upgraded package.

ADD COMMENTlink written 3.7 years ago by mapleforest10
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