Question: whole genome alignment using nucmer
0
gravatar for reza
9 months ago by
reza220
Iran
reza220 wrote:

hi

i aligned two whole genome using nucmer with this simple command

nucmer reference_genome.fasta query_genome.fasta

then three outputs files were created: out.delta, out.coordinates, out.tiling

Now, is there any way to know how percent of reference genome, covered by query genome?

ADD COMMENTlink modified 9 months ago by harishk020170 • written 9 months ago by reza220
4
gravatar for harishk0201
9 months ago by
harishk020170
harishk020170 wrote:

You can use dnadiff from the MUMmer suite actually. It will generate a .report file where all the details are present.

ADD COMMENTlink written 9 months ago by harishk020170
0
gravatar for lieven.sterck
9 months ago by
lieven.sterck6.7k
VIB, Ghent, Belgium
lieven.sterck6.7k wrote:

Not as such I think, you will have to post-process one of those output files (the out.coordinates if I remember well)

ADD COMMENTlink written 9 months ago by lieven.sterck6.7k

there you go :), I upvoted harishk0201 answer myself

ADD REPLYlink written 9 months ago by lieven.sterck6.7k
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