use chain to map from contig to chromosome

[ajo2995]

I have a browser instance displaying annotations on individual contigs, but I'd like to do on-the-fly coordinate system mapping to the chromosome level pseudomolecules once they are defined. There may be multiple versions of the pseudomolecules, so I'd prefer to just update my chains file instead of all the annotations.

I created a chain file to map between contigs and chromosomes based on an AGP file, but features are only being displayed from the first contig in a chromosome on my chromosome level browser instance. Is this use of a mapping chain out scope?

[dasmoth]

It's not quite what the system has been used for in the past, but seems entirely legitimate to me and sounds like you may have hit a bug. Certainly agree we should have a way of addressing use cases like this.

Time is currently limited but I should be able to have a look at this early next week. If you've got a couple of example files I could try, that would be super-helpful.

[ajo2995]

I’ve set up a page with the contig level browser and the chromosome level browser.

brie.cshl.edu/chain_test/ http://brie.cshl.edu/chain_test/

brie.cshl.edu/chain_test/contig2chr.bed http://brie.cshl.edu/chain_test/contig2chr.bed is there for reference.

On Sep 16, 2015, at 2:55 PM, Thomas Down notifications@github.com wrote:

It's not quite what the system has been used for in the past, but seems entirely legitimate to me and sounds like you may have hit a bug. Certainly agree we should have a way of addressing use cases like this.

Time is currently limited but I should be able to have a look at this early next week. If you've got a couple of example files I could try, that would be super-helpful.

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