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Please do not use comments to answer these questions. This proposal is not part of a Q&A site, and the task at hand is to help define what is on and off topic for a site. Comments are here to help improve the questions; not to answer them. See What is the rationale for deleting answers? Thank you. – Robert Cartaino Apr 18 '17 at 3:30

54 Example Questions (3 closed)

active newest votes

up vote 13 down vote

added by Imer Muhović Apr 15 '17 at 19:27

@A_Skelton73 Please do not use comments to answer these questions. This proposal is not part of a Q&A site, and the task at hand is to help define what is on and off topic for a site. Comments are here to help improve the questions; not to answer them. See What is the rationale for deleting answers? Thank you. – Robert Cartaino Apr 18 '17 at 15:48

up vote 12 down vote

added by sh4wn Apr 17 '17 at 15:35

Answers explaining why are potentially technical, which is good. Perhaps answers should highlight specific real-world applications where one is better than the other. – Koo Zhengqun Apr 18 '17 at 13:50

up vote 11 down vote

added by Franck Dernoncourt Apr 14 '17 at 14:45

up vote 11 down vote

added by Leonardo de Oliveira Martins Apr 15 '17 at 21:16

up vote 11 down vote

added by Scott Gigante Apr 17 '17 at 12:55

up vote 10 down vote

added by Franck Dernoncourt Apr 14 '17 at 14:45

up vote 10 down vote

added by user170884 Apr 15 '17 at 18:54

up vote 10 down vote

added by user172818 Apr 15 '17 at 19:16

maybe instead of 'best tool' asking about the best approach would be better? – Mitra Apr 16 '17 at 11:09

I think specific discussion should be held regarding, "can we post questions asking for a 'best tool'?" I do not think such a question is good, for example, at sites like CrossValidated (the statistics stack exchange). However, the bioinformatics field is new, new tools are being made rapidly, but discovering them is hard. I feel "good/best tool" questions are useful and appropriate here, but that is just my opinion. – ancientcampus Apr 18 '17 at 18:29

@ancientcampus The problem with such questions is that they age badly and are thus not helpful to people who reach them via search engines. The Q&A format doesn’t deal well with answers that are becoming obsolete fast. In fact, it’s a problem on Stack Overflow, and I don’t see how it would be solved here. – Konrad Rudolph Apr 19 '17 at 16:41

up vote 10 down vote

added by Leonardo de Oliveira Martins Apr 15 '17 at 21:27

up vote 10 down vote

added by gntc Apr 15 '17 at 23:14

up vote 10 down vote

added by user172818 Apr 16 '17 at 1:43

up vote 10 down vote

added by prab4th Apr 16 '17 at 9:21

This is one of these questions that could be on the borderline for Biology SE, no? (Just asking as I saw people downvote other questions which were more relevant for me to a Bioinformatics SE than this one) – Mitra Apr 18 '17 at 12:04

@Mitra I think it fits either platform. I’d even say that a (good) answer would potentially be different depending on the site. – Konrad Rudolph Apr 18 '17 at 12:08

That was my first hunch as well, but this question might get quite quickly controversial... – Mitra Apr 18 '17 at 13:11

up vote 10 down vote

added by prab4th Apr 16 '17 at 9:24

up vote 10 down vote

added by Konrad Rudolph Apr 16 '17 at 11:05

	A better question is why you'd want to do that? - What's your endgame? – A_Skelton73 Apr 18 '17 at 10:10
	@A_Skelton: Hm. I originally had a comment here linking to the original question. It provided ample context for why this was needed. Not sure why that comment got deleted. – Konrad Rudolph Apr 18 '17 at 10:51

up vote 10 down vote

added by Mitra Apr 16 '17 at 11:16

in retrospect, I wonder if this question could live on biology.stackexchange.com instead? (TBH, didn't know about Biology SE till a couple of minutes ago) – Mitra Apr 16 '17 at 15:32

It seems like biology.stackexchange.com is more geared for less technical questions – ahtmatrix Apr 16 '17 at 16:08

What type of sequencing? – Asker Brejnrod Apr 17 '17 at 15:08

up vote 10 down vote

added by Mitra Apr 16 '17 at 11:30

up vote 10 down vote

added by GWW Apr 16 '17 at 13:37

up vote 10 down vote

added by Mitra Apr 16 '17 at 15:22

up vote 10 down vote

added by Mitra Apr 16 '17 at 15:24

This question might fit better in biology than bioinformatics, since the answer will likely be based on evolutionary biology considerations. – bli Apr 18 '17 at 9:01

@bli Yes probably, but as I wrote in another question, I didn't know about Biology SE before. There is one reason I haven't deleted the question yet, is that the extent of this bioinformatics SE is not clear yet (at least for me). And as there is a bioinformatics tag in SO and Biology SE, one can argue that there is no real need for a new place anyway (with what I would disagree) – Mitra Apr 18 '17 at 10:50

What's wrong with including phylogenetics under the huge umbrella of Bioinformatics? It doesn't just have to be about high-throughput sequencing. – gringer Apr 18 '17 at 12:35

@gringer I agree with you about Bioinformatics is not only about sequencing and as pointed out by K.Rudolph in discuss.area51.stackexchange.com/questions/26711/…, we need to define this new SE. The reason I might agree with bli that this one should go to BiologySE is mostly due to the following question: Would "pure" biologists would consult Bioinformatics SE before designing their experiments? The fact that they should is pretty irrelevant though (at least for me) – Mitra Apr 18 '17 at 13:09

Phylogenetics is perfectly fine within bioinformatics. "wet lab" biologists may also be very well equipped to answer this question. I hope we don't start to develop a "one-drop rule" of biological purity. BTW for this specific question, the solution is computational (no lab experiments required). – Leonardo de Oliveira Martins Apr 18 '17 at 21:58

show 1 more improvement suggestion

up vote 10 down vote

added by ahtmatrix Apr 16 '17 at 16:09

up vote 10 down vote

added by gringer Apr 16 '17 at 22:46

up vote 10 down vote

added by gringer Apr 16 '17 at 22:52

up vote 10 down vote

added by gringer Apr 16 '17 at 22:56

up vote 10 down vote

added by gringer Apr 16 '17 at 23:00

up vote 10 down vote

added by gringer Apr 16 '17 at 23:05

up vote 10 down vote

added by abetusk Apr 17 '17 at 8:59

up vote 10 down vote

added by abetusk Apr 17 '17 at 9:18

up vote 10 down vote

added by abetusk Apr 17 '17 at 9:31

up vote 10 down vote

added by prab4th Apr 17 '17 at 9:31

up vote 10 down vote

added by sh4wn Apr 17 '17 at 15:58

Suggested rewording: "How can a set of reads be aligned to a population of genomes?" – gringer Apr 18 '17 at 20:42

up vote 10 down vote

added by Dominik Apr 17 '17 at 16:11

up vote 10 down vote

added by medbe Apr 17 '17 at 19:37

There is this thing of not asking about 'favourite' and 'preferred' tools, methods or papers... It might worth to narrow the question to a specific language or OS or on the other hand to extend the question to how the choice of a set of parameters is going to impact the final conclusion – Mitra Apr 18 '17 at 11:06

up vote 10 down vote

added by bli, edited by wythagoras Apr 18 '17 at 17:01

Note: I just changed the first word of this question, "s" to "Is" – wythagoras Apr 18 '17 at 18:26

up vote 10 down vote

added by bli Apr 18 '17 at 8:56

up vote 10 down vote

added by bli Apr 18 '17 at 8:56

up vote 10 down vote

added by Tom Aerts Apr 18 '17 at 10:36

On one hand: we're not supposed to ask about 'favourite' and 'preferred' tools. Also, this question, to my surprise, is googlable - you can find some libraries with moderate searching, though it's hard to tell what is "good" or "useful". Still, this is definitely a question worth discussing, and I would read it, so upvoted. – ancientcampus Apr 18 '17 at 18:26

up vote 10 down vote

added by gntc Apr 18 '17 at 18:16

up vote 10 down vote

added by ancientcampus Apr 18 '17 at 18:18

Further clarifications: the software is basically safe for such data. Basic concept behind this question: it's less of a technical question, more an issue that's fairly common and somewhat unique to bio/clinical informatics. – ancientcampus Apr 18 '17 at 18:41

up vote 10 down vote

added by gntc Apr 18 '17 at 18:20

up vote 9 down vote

added by DYZ Apr 14 '17 at 19:46

closed as not constructive by Konrad Rudolph, Aurora0001, Robert Cartaino Apr 18 '17 at 15:58

This question is not a good fit to our Q&A format. We expect answers to generally involve facts, references, or specific expertise; this question will likely solicit opinion, debate, arguments, polling, or extended discussion.

Whoever suggested to close the question as being not constructive: I specifically mentioned that the answer shall be evidence-based. – DYZ Apr 15 '17 at 21:55

That’s window-dressing. The question/discussion will be argumentative. From experience, it’s simply not a good fit for the Q&A format. – Konrad Rudolph Apr 16 '17 at 10:15

This could be answered with that one of these languages is most used in a career. Maybe changing to: "Which language is uesd most in bioinformatics"? – wythagoras Apr 18 '17 at 17:00