Introduction to bash for data analysis

[@Favour_Oyelami]

I've really learnt quick tricks for working on my command line in just this 26mins video. God bless you Dr.

[@valve_girl]

This is one of your first video I watched few days ago and now I'm in a streak to watch all lol

[@alishayan6905]

Great video. Thanks a lot for putting it out there! If you could please make a separate video highlighting the different applications of awk, it would be supremely helpful! Thanks again :)

[@aidanaguilera667]

This was super helpful and you made it easy to follow along. Thanks a lot!

[@jackycwwang]

Great intro to Linux beginners like me! Many thanks!!

[@upendra8050]

You don't have to use cat for piping to other commands. You can just use directly with those commands after pipe. For example instead of cat myfile.txt | cut -f 2 you could just do cut -f 2 myfile.txt.

[@MariaNattestad]

Thanks for your comment. I was keeping it simple to demonstrate piping for beginners and decided to show it this way since they are equivalent in nearly all cases.

[@ludosrex]

~ is called a tilde. At first your terminal did tell you what directory you were in. It is the home directory which is shown as ~. Mac is built on Unix. I’m glad you mentioned vim and nano.

[@SimonBaier]

If you already have a basic understanding of how to navigate and view files in bash, start at 14:45.

[@BiancaAguglia]

Great tutorial. It helped understand the power of bash. For data analysis I'll stick with Python and Jupyter notebooks, but I'll start using bash to manage the files on my computer. 😊

[@nabildhifallah6964]

yes it' important to get command from terminal .you have well showing to me what i need in my way of scientific and genetic researche thank you for you big effort done in this scientific domain

[@vladi1475S]

Great video! Very helpful and easy to follow! Thanks a lot!

[@danielromero-alvarez5392]

SUCH A FANTASTIC RESOURCE! THANKS! :)

[@RajeshKumar-dh9qu]

Thank you so much OMGenomics. It is really helpful and you make it so easy to understand. I like the Pokemon choice :-) My son is a big fan of Pokemon. I have a question: I have to work on bacterial genomes. Any Mac pro with 16 GB RAM is sufficient or higher RAM is required ? I would be using tools like Geneious software, web based tools and terminal.

[@mahmoudshaherchaher9938]

Thank you for the video! One quick question, please. The PS1 code didn't work for me to change the way the terminal works. Is that a common issue?

[@OMGenomics]

Is your computer running zsh by any chance? If so, check this out instead: omgenomics.com/adapting-to-zsh/

[@mahmoudshaherchaher9938]

@@OMGenomics Thank you very much! It's working now. P.S. I've replied twice to thank you and every time i write a reply, it gets deleted for some reason :D

[@hubstrangers3450]

Hi Good to observe someone from life science really presenting basic programming skills, however would strongly suggested stick avoid GUI, return to visualization only when substance need to be explained in greater depth. Command line and coding skills (logic, functions, libraries etc), would suffice, folks with scientific bacgrouds will be able to figure out there rest. For CS folks.. life sciences is million miles away from their horizons

[@andriekusnadi7693]

Is this gnu bash?because i use gnu bash on fedora and ubuntu linux?

[@mohammadwaqasshahid4703]

How do i do this on ubuntu? mine gives error when i use the open ~/.bash_profile command. it says open is not a command Can you please help? Thanks

[@OMGenomics]

Edit with vim or your favorite text editor instead.

[@chakavak2015]

Great video! Thank you very much!

[@bitoksot2863]

Thanks for the great info, I am a beginner to this field of bioinformatics and was just wondering...why do I need to start getting used to Mac/Linux OS considering that I have been using Windows like 'forever' now...and do I really have to change from being a windows user to a Linux user?

[@OMGenomics]

If you are working with large files on your institution's cluster or the cloud, or running NGS analyses, then you will mostly be working on the command-line. Windows machines have their command-lines in DOS, which won't run the bioinformatics pipelines that were all written for Linux/Unix. That means that most bioinformatics pipelines will run on a Mac just as well as on a Linux server, but they won't run natively on Windows, so you can run those tools on your institution's cluster or on the cloud instead, which you would probably be doing most of the time anyway. Mac users just have the added bonus of being able to feel like a hacker on their own computers, jumping around the file system and manipulating files like they do on the big servers. I typically don't run pipelines on my Mac (because they use huge files, many cores, etc.), but I do a lot of little things, including stuff like the mini-analyses I showed in the video.

[@elhipster1]

fantastic video super helpful!

[@franciscoromogaray3076]

Te rifaste gÜerilla muy bueno, sirvio de repaso.

[@mehrdadrabiei5785]

Can we do analyze in Linux command line?

[@muzahirhussain8819]

i try to do this but it didn't work, is it because im not working on mac ? or something else agha@agha-TravelMate-4730:~$ touch ~/.bash_profile agha@agha-TravelMate-4730:~$ open ~/.bash_profile Command 'open' not found, did you mean: command 'gopen' from deb gnustep-gui-runtime (0.27.0-5build2) command 'pen' from deb pen (0.34.1-1build1) command 'wopen' from deb gworkspace.app (0.9.4-2) Try: sudo apt install Can you please guide me, whats wrong

[@OMGenomics]

Yes it may only work on Mac. Try using vim or vi instead (may need to google some instructions for these), and also check if the ~/.bashrc file is called something else on your operating system. You can also skip those first steps if they don’t work, since they’re not required to follow the rest of the video, just helpful in general.

[@muzahirhussain8819]

@@OMGenomics thanks for your quick reply, i will look into it and come back to you.

[@GijoeXD]

I think it is bad that bash is configured so poorly by default. I stumbled over this phenomenon on the mac of a friend. He asked me to fix something since i am familiar to linux and mac is basically the same. Why could apple not simply copy the config from a linux distro? They are using a linux shell anyway.....

[@mosiotv]

Thanks a bunch, very helpful, subbed! Can you please continue your linux tuts? You do it like no one else, so exact and pinpointing!

[@yukifujishima]

Hi Maria, thank you for the great video. How can I change the colour of texts back to the original??

[@marcelodiasable]

Place this line between the colors: local NONE = "\ [\ 033 [0m \]" # Default Replace the line with this: $ " For this: $ ${NONE} "

[@yukifujishima]

Thank you mate!

[@nmertsch8725]

(How) Can I follow along on my Windows PC? It seems to be a great tutorial though...

[@nmertsch8725]

Okay nevermind, new versions of Windows 10 64bit support a "Bash on Ubuntu on Windows", which emulates a bash in the cmd (at least this is what it looks like for noobs like me). "open" does not work, as it obviously can't find the default applications of Ubuntu, but vim or nano also do the job. Thanks a lot for this, it is quite hard to find good tutorials for total beginners!

[@OMGenomics]

Glad you found a way! For others who see this: To use bash you do need somewhere with a Mac or Linux OS to enter the code, which can often be in an institution's cluster where you have data stored and are running software from anyway. If any of you want to practice and don't have a computer system at your institution to ssh into (or a Mac/Linux computer), you can always use a virtual machine and install a Linux OS on it, and practice in there: www.virtualbox.org/wiki/Downloads

[@amnghn]

For me, it doesn't change the colour at all!

[@OMGenomics]

Is your computer running zsh by any chance? If so, check this out instead: omgenomics.com/adapting-to-zsh/

[@amnghn]

@@OMGenomics Yes, now it works perfectly. thank you so much.

[@lyingcat9022]

Tilde!!! Haha it’s the symbol above he Spanish letter ñ. And it’s pronounced “til duh” not “squiggly” ;) haha Great vid by the way!

[@OMGenomics]

Haha, you know it’s funny how nobody caught that was a joke... trying to make the field more welcoming and less perfectionist about the little things. Oh well.

[@lyingcat9022]

OMGenomics haha yeah I figured you were just messing around. I was just busting your chops ;) Also clarifying Incase someone didn’t know. Great content, thanks :)

[@Tech.Library]

@@OMGenomics great video. But all u have done on the data of pokemon can easily be done with excel with ease. Any thought?

[@mohamedesmailelsalahaty6050]

Thanks dr

[@derekfrost8991]

Great tutorial but I wouldn't use bash for any datasets.. :)

[@haraldurkarlsson1147]

Clearly exaplained.

[@hendadel8042]

Please I want to contact you ASAP , I need some help

[@diarrassoubamamadou6775]

so good tuto can i get you mail? i want to ask somethings on my bash scrip

[@bumbudo]

i had to modify my script because it turned my terminal text black on a black background so i couldn't see it. function prompt { local BGreen='\e[1;32m' # Green local BIBlue='\e[1;94m' # Blue local NONE="\[\033[0m\]" # Default local GRAY="\[\033[0;37m\]" # Gray local BYellow='\e[1;33m' # Yellow local BLACK="\[\033[0;30m\]" local CYAN='\e[\033[1;36m' export PS1=" ${BGreen}\u${BGreen}@${BGreen}\h:${BIBlue}\w${BLACK} $ ${NONE} " } prompt

[@bumbudo]

i also now have had my bash cursor shifted once to the right after using this code... any ideas why?

[@bumbudo]

also thanks for your vids, they're awesome!

[@bumbudo]

hm it took some tinkering with the code but no more space before my cursor anymore... don't know exactly what it was but it is all in order now