linux for genomics

Question

[vaishnavi]

hi everyone,

I have just started learning genomics as a part of my bioinformatics degree and I've been introduced to linux for handling fastq files and using fast qc. can anybody suggest some good learning resources which is more inclined towards linux for genomics.

[boczniak767]

Maybe this link from SeqAnswers will help.

[Ram]

That SeqA post is insanely dated.

Vaishnavi, you'll need to Google around but the good news is, you need to understand just the basics of linux in the bioinformatics field. You'll rarely even get to using root-level commands. I'd suggest searching the site for unix/linux-related posts and looking online for basic Linux command tutorials, plus using man on as many commands as you can while trying examples.

Start off with:

1. cd, ls, mkdir, echo, cat, head, tail
2. find
3. grep, awk, sed (basics)
4. shell scripting, screen/tmux (screen is easier IMO and is really useful in keeping commands/command-sequences isolated in their own "environments"
5. if, for constructs
6. xargs
7. gnu-parallel

I'm quite good at linux (even if do say so myself) but commands wise, I do not know (off the top of my head) much beyond the building blocks I've listed above. I google when I can't find a command to get a task done, and 99% of what I need to do can be built using these blocks.

Later, you may also wish to learn HPC or AWS environments so you can run your commands on a cluster/on the cloud.

[ctseto]

This one may feel a little basic, skewed towards newcomers, perhaps much more fundamental. But nothing wrong with making sure fundamentals are in order!

https://www.futurelearn.com/courses/linux-for-bioinformatics

Answer 1

[GenoMax]

This UNIX primer from Korf lab is an excellent resource to get started.

Titus Brown's NGS data analysis workshop is also a great resource.

Answer 2

[JC]

The Linux Documentation Project has many resources to read

Answer 3

[4galaxy77]

My advice would be (to echo Ram) focus on a subset of small command line commands and don't worry too much about learning about the nuts and bolts of Linux. In a rough order of importance I would say learn the following:

1. cd, cat, mkdir, ls -lh, rm, touch, head, tail, echo, find, man, ../, sudo
2. cut, for, while, if else
3. grep, sed, awk, parallel

Answer 4

[Mensur Dlakic]

As you were told already, it may be a good idea to become Linux-proficient first. Many summaries of main Linux commands are available in 1-4 page formats if you Google linux cheat sheet or linux command reference.

Online courses, in lecture format:

• http://www.doc.ic.ac.uk/~wjk/UnixIntro/
• http://tldp.org/LDP/intro-linux/html/
• http://www.ee.surrey.ac.uk/Teaching/Unix/