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Bioinformatics for Genomics Course – University of Padua

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quiz

Lab02/0: First quiz

This post is a part of the second laboratory session. Please refer to the main post.

First quiz for the practical: check how much did you learn about the terminal and its commands

The following command:

mkdir My Directory

Will create a new directory called “My Directory”

If I wanted to create a “My Directory” new directory, I had to add quotes around the two words.

Will create a directory called “My”

Will move “My” to “Directory”

In your home you have two directories: lab1 and lab2. You are currently working on lab1 and want to list files present in the lab2 directory. Choose the right command(s):

ls lab2

cat /home/lab2

ls ../lab2

cat ../lab2

cat lab2

The following command:

grep > genome.fasta

Print only lines containing the > in a file called genome.fasta

Will redirect the output of the “grep” command into a file

The genome.fasta file will contain some lines after the execution

If the genome.fasta exists before the command, will change after the command execution

The command head will print the first 10 lines of a file. To print the first 100:

head filename -n 100

head -n 100 filename

head -n100 filename

head filename | tail -n 100

To count how many sequences you have in “genome.fasta”, you can:

cat genomes.fasta | grep “>” | wc -l

grep > genomes.fasta | wc -l

grep “>” genomes.fasta | wc -l

wc -l “>” genomes.fasta

grep “>” genomes.fasta > lines (and then) wc -l lines

less “>” genomes.fasta

If you want to see how many files (or directories) you have in your home folder:

ls ~ | wc -l

ls /home | wc -l

ls ~ > wc -l

ls ~ > ls (and then) wc -l ls

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Question 1 of 6

Tagged bash, quiz

laboratory

Lab02/1: A small recap and more on pipes and stuff

This post is part of the second laboratory session!

We are going to start with a refresh of Bash command, and possibly learning some new one.

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Tagged bash

laboratory

First practical

Welcome to the first practical. During this practical you’ll learn how to master the command line and Linux as well.
Please, keep in mind that all the tools we are presenting day by day are necessary to fulfil the final assignment, so try to think about all the steps rather than rushing to the end.

Feel free to ask us, in case of troubles…

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Tagged bash, command line, laboratory

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