For bioinformatics, which language should I learn first?

Whether you are a wet lab biologist wanting to add some bioinformatics skills to your toolbox or if you are trying to get all the way into bioinformatics and make your own software, I have some concrete recommendations about what programming languages to start with. I focus on R, Python, and Bash for beginners, and I also consider in what circumstances you should consider adding other languages, including C, C++, Ruby, Java, PHP, JavaScript, and Matlab.

[kareemjeiroudi]

Yeah, please start making tutorials for bioinformaticians.

[quocledoan]

2020 and still valuable advice. Thank for your helpful information, it helps newbie like me to determine what to learn and practice.

[km]

i use R in bioinfromatics, and will learn bash and increase my linux skills, thanking you for the valuable advise maria

[SomnathRoy]

Thanks Maria for the videos and tutorials. I would love to learn how to use sequence data from databases, choosing a subset from the whole data, and how to proceed step by step through different genome analyses. I'm a plant breeder and have experience in R for data analysis in R.

[geocarvalhont]

Nice!!!! Maria, thank out for starting this project. I was waiting for someone with experience start a channel talking about bioinformatics, especially clinical bioinformatics! So, is a pleasure see your videos.

[michaelburns]

Just found your channel - awesome info! I'll be sending students here.

[lhtd]

I switched from molecular biology to bioinformatics. I must say that understanding programming was way easier with python, which allowed me to go further and faster in R, compared to people who started straight forward in R. My advise is, go for python to understand programming, and if you can, go as quickly as you can to object programming in python. Then go to which ever language you like. Understanding a little bit of classes and stuff will become really helpful when you'll debug your code. Because you will be debugging your code ! :-) -- Nice video, thanks :-)

[joshua]

Python is the absolute king of string handling, this is a must learn language - but you can learn it in hours.
R is an absolute must. R sucks in so many way - it fails silently, it is hopelessly fragmented, it will produce unexpected results, and fill large data sets with unexpected formats and characters. No matter how experienced you get, you will still find your data unexpectedly converted to factors (a loss of information), or stripped of identifiers, or some other outcome because the author of some essential package decided it was OK to break your data in a way they do not care about.
Learning basic R is like torture, and it invites the worst programming habits one can imagine, and these horrible habits are transmitted into the various packages making them even harder to learn. Then you have to deal with R programmers to answer questions, and these people are the worst of all the worst people on Stack Overflow.
A word of warning to newbies in R for bioinformatics. Avoid dplyr - you will put alot of work into creating data frames that are formatted in ways that packages require, and dplyr will silently remove some of these formats (row names in particular). All the ease of using dplyr is undone by have to add extra lines to reformat that data frame

[ayoelegs]

Thanks so much Maria for the great videos.

[BIueKiji]

Being a student in bioinformatics who will soon learn Python, and since it does seem really useful, I would really appreciate videos on it !
It was a cool first video, I'm looking forward for more !

[nihalelrouby]

Very nice and useful video. It would be great to do a tutorial on how to use bash to run pipelines such as Next gen or RNA sequencing pipeline.

[skepto]

I really can relate to you. My background is in molecular biology but I want to switch to bioinformatics. Currently reading practical computing for biologist book and learning bash.

Also,  I found some people suggest to learn some db management..like SQL, what you think?

And good luck with your company, wish you all the best 😀

[aaamog]

Hi Maria, thank you so much, very informative and helpful videos. I'm a graduate student, I have done my B.Sc in Biotechnology and now I'm getting started with Bioinformatics. My thesis is in the field of microbiome analysis and I already took an online course in bash and R. I would be glad if you can make a video analyzing data from metagenomics sequencing, covering methods like MetaPhlAN v2, assembly of raw data, binning, gene prediction etc... Thanks, Angel.

[NaSarGR]

Hello Maria, I really like your videos as they are quite comprehensive. I was wondering as a computer engineering undergraduate how difficult will be a transition to bioinformatics . I have a background in computer science and a good knowledge of all these languages you referred to in your video except of R which I have only used a few times in the past. So I plan on moving to the US as a grad student in the next two years and this field of bioinformatics is really a big concern to me.

[kenoskyiscool]

I majored in biology during undergrad, bioinformatics in grad; where I learned Perl, Java, and R. Python may be the future (or, some say that Julia is the future) but Perl is still the industry standard, currently. If you are coming into bioinformatics from a CS major, learn Perl. However, bioinformatics is an umbrella term and truth is that which one you will mostly use is going to depend on what type of bioinformatics you will be doing, and, what lab you join.

Anyways, my opinion is to learn Perl first. Maybe C++. Python is awesome, sure, but you are almost forced into how you will write code/scripts. Perl forces you to think like a computer scientist and to think analytically about the code you are about to write. Yeah, it may be sloppy at times, but you get a better appreciation for what is going on. Python is like iOS: there is only one way to do it and that way is the way that Apple wants you to do it -- no Terminal -- just a push a few buttons to get things done. Perl is like OSX/macOS: you have access to Terminal, and all that comes with it. Among many other things that you cannot do with iOS, with Terminal you can build your own trees and pathways. Sure, you may accidentally delete a pathway, or, create a pathway only to later forget "where" it is, but hey, way more powerful, though. And yes, Perl can also be like Linux.

[ghaidaahmed]

Yeah, I would like to know more from you about R, python and bas.

[jayalalkj]

Thanks for the video. I am a Master student in Genomics and systems biology, I just started R and Perl. Most of my classmates say. Python is better than Perl. What do you recommend Perl or Python?. in this video you talk something about Bash-I want to develop tool- which is to find the bacterial community and their related functions, with NGS data. How bash could help me to complete my goal!...Sorry if I am wrong ..

[QingzhouZhang]

Simple and straight forward!
Although, I, myself, started bioinformatics career with web applications, :-P, but still not recommended web programming for beginners.
Thanks for the show!

[mobina]

This video was really useful for starters like me. Tnx

[Eagline]

The datframe you are talking about are natively supported by numpy array which is included in python but in the form of included package, panda is just a tool for no pure CS person