about 3nt periodicity output

[Jiahuan90]

Hi Saket, Thanks for developing this great tool!

I have a question on 3nt periodicity:

I used ribotricer find many ORFs in lncRNAs. However, I found adjust parameter would give different number of ORFs on lncRNAs.

Therefore, I want to draw periodicity on some lncRNA's ORF to check if lncRNA's ORF have false positive.

I don't know how to use ribotricer to meet my requirement.

Thank you for your kindly help~

[saketkc]

Hello @Jiahuan90, thanks for the question. I have created a notebook to demonstrate how to plot ribotricer generated profiles: https://github.com/smithlabcode/ribotricer/blob/master/notebooks/Plotting_ribotricer_profile.ipynb

Feel free to reopen if you have any follow up questions. Thanks!

[Jiahuan90]

Hi @saketkc, thank you for your kindly help!

I've realized that column 18 ---- profile from *SRX219170_translating_ORFs.tsv are reads coverage of each nucleotide.

However, I have another question: I've carefully look through the manual, finding that, by default, ribotricer doesn't take read coverage into account when detect ORFs. The key element is the phase score.

I try my best to study the paper "Accurate detection of short and long active ORFs using Ribo-seq data", but still can't understand the concept of phase score.

I was wondering if it is possible to explain the concept of phase score?

Thank you again for your kindly help!!

[saketkc]

These slides might be helpful: https://saket-choudhary.me/pdfs/ribotricer_concept.pdf (there are transitions so ideall best viewed in slideshow mode) => The idea is to essentially calculate how often the profile exhibits the "high-low-low" pattern.

[Jiahuan90]

These slides might be helpful: https://saket-choudhary.me/pdfs/ribotricer_concept.pdf (there are transitions so ideall best viewed in slideshow mode) => The idea is to essentially calculate how often the profile exhibits the "high-low-low" pattern.

Hi @saketkc, thank you for your kindly help again!!