Hello World,
Thank you for all the support provided till now.
I am adding annotation information for a variant call data. Did VEP for the same. Apart from feature type which is given in VEP output is there any easy way to find the which feature the position belongs to? Some other easy method than overlapSelect.
You can simplify your VEP output by asking for the "most_severe" consequence only. This means that you'll just get one consequence per gene. This could make your VEP output more along the lines of "what kind of feature does it overlap?", rather than the detailed information you're getting now. You can do this with both the web tool and the standalone script.
Thanks a lot Emily.
Currently I am getting feature type 'Transcript' only using Variant Effect Predictor annotation. So if I simplify VEP output by asking for the "most_severe" consequence is there chances that I may get the specific feature like 'Exon, UTR, repeat region' etc.?
The consequence defines exactly where it hits. So something with the consequence "intron_variant" falls in an intron. "Missense" tells you that it falls within a coding exon and changes the amino acid sequence. The definitions of these terms are listed here.
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Welcome to BioStar! Unfortunately your question does not look answerable in its current state. VEP is probably not common terminology for many users on this site and the internet---it certainly isn't for me. Please provide some more detail there. Also, your question isn't very clearly stated, so anything you can do to clarify what your specific problem is will help the community to help you.
Variant Effect Predictor - very common terminology for BioStar users, particularly those working in variant annotation who are likely to read this question and think it's relevant to them. This question looks perfectly legible to me.
Welcome to BioStar. I'm sorry your first experience was someone being unnecessarily rude to you.
Wow Emily, please point out precisely where I was rude, or how my suggestions would not improve this question for all current and future BioStar users.
You told this person their question was not clear and was unanswerable, when it is completely clear and answerable. So in terms of your "suggestions" improving this question would go, I didn't really spot any suggestion other than telling the OP to clarify a term that you (unlike many others on BioStar) are ignorant of.
If I did think a question was not clear, I would certainly not tell someone "your question is unanswerable" because to do so is confrontational and rude. Instead I would ask them specific questions about what they were trying to do, such as "Could you explain what you mean by...?" Thus, I am implying that I am ignorant and I need further explanation, not that they are doing something wrong. Your position is to say "You're in the way," to someone you want to walk past, which is rude, mine is to say "Excuse me, can I get past please?"
Lastly, if somebody is asking questions using the names of bioinformatics tools, if I am not familiar with those tools, I tend not to respond to the question. If I don't know what tool they're talking about, then that question is not for me. I certainly don't bowl into discussions on things I don't understand, telling people off for not spelling out all the jargon for me.
I follow the
gff3tag, which is why I was notified of this question in the first place. I have extensive experience with genome annotation and working with annotation data in a variety of formats. I've also done a bit of variant calling, although I will admit that I have much less experience with this than with annotating protein-coding genes. So if you want to talk about being rude, perhaps you can explain how you're sure that I'm the only one on BioStar that's unfamiliar with the VEP term.I concede that had I been more tactful and specific in my original feedback, it would not have been as rude. It certainly was not intended to be.
And regarding your analogy about who is in whose way, in a Q&A site like this users have to meet each other half way. Those posting answers have a responsibility to be welcoming and to put forth a fair effort to understand and respond to questions. Those posting questions have a responsibility to post questions that are detailed and specific, written clearly and simply.
As far as my specific concerns for this post, the title doesn't seem to agree with what's being asked in the post (feature type vs the precise feature), so I wasn't sure I had read it correctly. And then there was some awkward wording ("...easy way to find the which feature...") and some sentence fragments. And finally the fact that I was unfamiliar with VEP, although apparently I'm the only one on BioStar...All of these concerns together is why I claimed the question was not clear. Apologies for not being more specific.
And sorry Vineeth for highjacking this thread. I'm sure the last thing you wanted to see here was a lengthy discussion on Q&A ethics...
Thank you Daniel Standage for the suggestions which will help framing clear questions.
Perhaps Vineeth doesn't ask questions in the way that you would, but that doesn't mean he is asking them incorrectly. I understood his question. His title lead me to read his question, thinking it might be something that I would be able to answer, and it turned out it was. If that's not the definition of a well written question and title then I don't know what is.
I don't know how many people on here understand the term VEP, but a quick search gives me two pages of results. From that, I'm going to guess, a reasonable proportion. Whether I understand a term or not, I would certainly not tell someone that a term wasn't common terminology without checking first.