ORF segmentation (AUG vs non-canonical starts)

dieterich-lab / rp-bp

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.

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ORF segmentation (AUG vs non-canonical starts) #80

Open CDieterich opened 7 years ago

CDieterich commented 7 years ago

We noticed in a head-to-head comparison of ORFs predicted with canonical and non-canonical starts that some longer ORFs with non-canonical starts do not have any supporting reads in the extended 5'part.

We should think about on how to deal with this.

m-swirski commented 6 years ago

Yes, I have seen the same thing. In fact It happens for most ORFs once alternative codons are being searched for. Are there plans to fix this?

eboileau commented 6 years ago

This is on our to-do list and should be addressed soon. If you have any relevant examples, please don't hesitate to post these here.

m-swirski commented 6 years ago

I have looked closer into the profiles and it seems that the problem doesn't lie in 'no reads at all' but small fraction of them compared to other potential TIS (or annotated one).