Introduction to bash for data analysis

For absolute beginners. Using the command-line/shell/terminal for basic data analysis. This video covers how to find the terminal, navigating around the file system, looking at files, editing files, and even using piping to string together different commands and unlock the power of bash.

[Favour_Oyelami]

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

[sylvaniathehacker]

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

[SimonBaier]

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

[upendra]

You don't have to use cat <file name> for piping to other commands. You can just use <file name> 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.

[nabildhifallah]

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

[jackycwwang]

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

[aidanaguilera]

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

[alishayan]

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 :)

[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. 😊

[vladiS]

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

[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.

[mehrdadrabiei]

Can we do analyze in Linux command line?

[hubstrangers]

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

[mahmoudshaherchaher]

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?

[andriekusnadi]

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

[mohammadwaqasshahid]

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

[RajeshKumar-dhqu]

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.

[yukifujishima]

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

[bitoksot]

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?

[muzahirhussain]

i try to do this but it didn't work, is it because im not working on mac ? or something else

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 <deb name>


Can you please guide me, whats wrong