-
Notifications
You must be signed in to change notification settings - Fork 1
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Peptides at the transcript end not excluded #649
Comments
So we are talking about coding and noncoding transcripts with known end but stop lost mutation? I feel like 1) is worth a run-through until the end of the transcript. |
The question is about whether we should include the very last peptide or not. I guess it's a yes because the transcript sequence is known and it's also known that the transcript stops at the given position? |
I think overall if it's just the very last peptide it's not going to make a huge difference. But there are a few different cases that we have to treat differently? I think c) and d) are the cases where we are worried about the last peptide? for a) and b) we need to decide whether we want to stop at the stop codon |
For a peptide at the very end of the 3' end, there isn't anything downstream at all. For for coding transcript, the case would be, if there is a stop lost mutation that causes the 3' UTR being translated, should we include the peptide translated from the 3' end. For noncoding, there is not UTR at all, so the issue would be if there isn't any stop codon after the last start codon, should the very last peptide be included. One situation that I can think of to not inclulde the last peptide is circRNA. In mpg, we represent the circRNA as linear graph with the sequence copied 4 times. But the very last peptides should not be included. Agreed that this is not going to change much! But it's currently not handled consistently so I want to clean it up. |
OK we can separate coding and noncoding Coding
Noncoding
|
That aligns with my thoughts, too! How about circRNA? Do you think we should also include the very last peptide? |
…end of the transcript sequence) are now excluded for transcripts with the `mRNA_end_NF` tag and circRNA regardless of it. Otherwise for transcripts (either coding or noncoding) that the mRNA end is confirmed (without the `mRNA_end_NF`) they are now included in the final FASTA. #649
Based on a discussion that we had a while ago (maybe > a year) that we want to exclude the peptides that are at the very end of the transcript if the end of the transcript is not confirmed (with
mRNA_end_NF
). But there are two cases we need to consider:For the above two situations, should we also ignore the peptides at the end of the transcript?
The text was updated successfully, but these errors were encountered: