mahulchak
commented
4 years ago Sorry for the confusion.
Donor = reference = self
If you use standalone quickmerge, the order of reference and query does not matter as long as you use the correct switches (-r for reference and -q for query).
Let me know if you need more information.
On Wed, Jul 31, 2019, 01:36 Bob Harris notifications@github.com wrote:
Which is first on the command line?
This may sound trivial, but to someone like me who is trying to figure out which of my assemblies I should give first on the command line and which second, it isn't helping that every time the assemblies are discussed they have different names.
The NAR manuscript uses both donor/acceptor (which to me seems the most informative) and reference/query. It seems to mostly use reference/query in discussion but figure 4 only uses donor/acceptor.
In description of how to run the wrapper, the main readme here calls them hybrid and self. I have yet to figure out which of those is the donor (a.k.a reference) and which is acceptor (a.k.a. query).
The manuscript also says it merge a hybrid and a pacbio. If the paper tells me which was donor it has eluded me.
The quickmerge wiki gives some advice for deciding which of my assemblies should be the query, and which reference. But, it fails to tell me which order these should appear on the command line.
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rsharris
Which is first on the command line?
This may sound trivial, but to someone like me who is trying to figure out which of my assemblies I should give first on the command line and which second, it isn't helping that every time the assemblies are discussed they have different names.
The NAR manuscript uses both donor/acceptor (which to me seems the most informative) and reference/query. It seems to mostly use reference/query in discussion but figure 4 only uses donor/acceptor.
In description of how to run the wrapper, the main readme here calls them hybrid and self. I have yet to figure out which of those is the donor (a.k.a reference) and which is acceptor (a.k.a. query).
The manuscript also says it merge a hybrid and a pacbio. If the paper tells me which was donor it has eluded me.
The quickmerge wiki gives some advice for deciding which of my assemblies should be the query, and which reference. But, it fails to tell me which order these should appear on the command line.