Closed SHuang-Broad closed 3 years ago
The idea would be that for RNAseq data, you might want allow for the potential for skipping introns (or gaps). So that if you once you hit a deletion of a certain size, you might want to reduce the penalty.
So, for example, you might allow a deletion of 10bp, but after that, you’d have no penalty.
I’m not sure how practical it ends up being in practice though.
— Marcus
On May 5, 2021, at 2:41 PM, Steve Huang @.***> wrote:
Hi Marcus,
I'm wondering what the intuitions are behind the gap extension decay parameter?
In particular, I've noticed the use of that parameter is modeled as
min(0, self.gap_extension_penalty + ins_run * self.gap_extension_decay) and similarly for deletions.
My guess is that this is to further discourage large gaps? Is there a specific use scenario you had in mind for this model?
Thanks! Steve
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Ah, I see. I assumed it was for DNA. Thanks for the quick answer! Steve
Hi Marcus,
I'm wondering what the intuitions are behind the gap extension decay parameter?
In particular, I've noticed the use of that parameter is modeled as
and similarly for deletions.
My guess is that this is to further discourage large gaps? Is there a specific use scenario you had in mind for this model?
Thanks! Steve