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smithlabcode / ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data
http://doi.org/djv4
GNU General Public License v3.0
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Prepare ORFs step #152

Closed bshim181 closed 1 week ago

bshim181 commented 4 months ago

I had a question regarding preparation of all candidate ORFs from annotated transcript regions. I was wondering why only 3 frame translation is conducted to pull out candidate ORF. If I am trying to generate a database of ORFs from my transcript targets of interest, does it make sense to do 6 frame translation to get all candidate ORFs?

danielrebib commented 2 months ago

No, because the "negative" three frames would mean your transcript is read from 3' to 5' direction, which doesn't occur to a processed mRNA. Given that you already know the strand of the parent transcript (as they are all annotated ENSTs), then you know the direction they must be read in.

saketkc commented 1 week ago

thanks @danielrebib! @bshim181 the index also takes GTF as an input which has the direction of translation for these genes (since these are annotated)