inverted D annotation

[Elizabeth Van Itallie]

Hello,

Does partis consider the possibility of 3' -> 5' orientation of D segments? if not, do you think there would be issues with putting a 3'-> 5' D sequence in the reference file, where this also the 5' ->3 ' orientation, as a different D "gene" ? 

Thanks!

-Elizabeth 

[Jesse Connell]

That can happen?!  I thought D and J were all oriented the same way and just V were in mixed orientations.  (Or is this a situation where I'm not yet up to date on all the possibilities of VDJ recombination?)

Jesse

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[Duncan Ralph]

It doesn't consider them, no, but you're correct that just adding reversed D sequences to the D germline fasta will work fine. You could add anything this way, e.g. concat'd D genes for VDDJ.

As to whether/how much it actually happens, I don't know.

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