Intro to UNIX: Glossary

Unix is the single most powerful tool in a bioinformaticians toolbox.

Use pwd, ls, cd, cp, mv, mkdir, rm, man, cat/zcat, echo to list, move, copy, and view files and directories

Use > to redirect stadard output to a file

Use | to redirect standard output to another program

Use <command>& to run a program in a background

Use jobs to see jobs you are running in a shell

Use $() include an output from a program in a string

Use wget and curl to download data

Use head and tail to inspect data

Use less to view data and to build pipelines

Use wc, ls, and awk to obtain data summary

Use cut to select specific columns

Use grep to search for patterns

Use sort to sort data and unique to find unique records

Use sed to edit data streams

Use $() to include an output from a program in a string

Don’t forget the proper header in your scripts

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