T3-2024-Bioinformatics-BASh-Jeopardy

Moving Around

100

pwd

What is my Present Working Directory

200

mv my_file.txt ../this_file.txt

What is move <file> up one level and rename as <new_file>

300

cp /home/genome/joseph7e/reads/*.fastq.gz ./

What is copy all my fastq files from all directories to my current directory?

400

Name the path type:

1.) /home/genome/joseph7e/my_dir/

2.) ../genome/joseph7e/my_dir/

3.) ~/ (hint: sort of a trick question)

4.) ./

what is absolute, relative, absolute, relative?

500

cd /
cd home
cd users/

cd $USER

what is moving into my home directory

Peeping

100

nano file.txt

what is a way to edit a file?

200

less -S textfile.txt

What is the best way to view a text file without line wrapping?

300

gunzip my_reads.fastq.gz

Unzip the fastq file

400

cat *.fastq.gz

what is a terrible idea?

500

grep '>' fasta.fasta | head | tail | head | tail | head

print the first ten lines of a fast file.

Fun with grep

100

grep "one" <file>

What is a way to display every line in <file> that includes one.

200

history | grep qiime

What is display all the lines form your history that include 'qiime'?

300

grep '>' contigs.fasta | less 

What is display all the headers in my contigs file?

400

history | grep qiime | grep beta

what is print all the commands that contain the word qiime and beta?

500

awk -F'\t' '$2 > 10000 && $5 > 50 {print $7}' | grep "grep" | sort | wc

separated by a tab character print only lines that are greater than 10000 in column 2, greater than 50 in column 5, print column 7, grep for lines containing grep, sort them, print the number of lines.

What's In My File

100

I open it with iTOL

What is a phylogenetic tree. tree.qza

200

>header

ATGCGATGGATGCA

>header2

ATGGTCAGTA

What is a FASTA file? (specifically a multiFASTA)

300

@Filename

GATCCT

+

IGICVW

What is a FASTQ?

400

This file includes per sample counts for each unique sequence variant.

What is a feature table (OTU table, SV table)?

500

5 common bioinformatic file formats

.nwk

.fasta

.gff

.faa

.fastq

Tricky Tricky

100

man echo

What is show the manual for the command echo?

200

Reads are broken up into these short fragments of the same length for spades assemblies

What is k-mers?

300

"which blob_blast.sh" will output this

What is show the absolute path to the blob_blast.sh script on the server?

400

The first line of a bash script starts with this symbol (#!)

What is hash bang or she-bang?

500

The difference between $1 in an awk command and $1 in a bash script

What is awk refers to column 1, bash refers to the first parameter passed to the script