Moving Around
pwd
What is my Present Working Directory
head file.txt
print the first ten lines of a file.
man echo
What is show the manual for the command echo?
grep "one" <file>
What is a way to display every line in <file> that includes one.
I open it with iTOL
What is a phylogenetic tree. tree.qza
mv my_file.txt ../this_file.txt
What is move <file> up one level and rename as <new_file>
less -S textfile.txt
What is the best way to view a text file without line wrapping?
cal -help
What is show the help menu for cal?
history | grep qiime
What is display all the lines form your history that include 'qiime'?
>header
ATGCGATGGATGCA
>header2
ATGGTCAGTA
What is a FASTA file? (specifically a multiFASTA)
cp /home/genome/joseph7e/reads/*.fastq.gz ./
What is copy all my fastq files from the directory to my current directory?
gunzip my_reads.fastq.gz
Unzip the fastq file
whatis cal
What is show the one line description of the calendar program?
grep '>' contigs.fasta | less
What is display all the headers in my contigs file?
@Filename
GATCCT
+
IGICVW
What is a FASTQ?
Name the path type:
1.) /home/genome/joseph7e/my_dir/
2.) ../genome/joseph7e/my_dir/
3.) /home/user/share/
4.) ./
what is absolute, relative, absolute, relative?
cat *.fastq.gz
what is a terrible idea?
How do I run qiime if I have a non-16S data and I dont know where to start?
What is google?
history | grep qiime | grep dada2
what is print all the commands that contain the word qiime and dada2?
This file includes per sample counts for each unique sequence variant in a metabarcoding file.
What is a feature table (OTU table, ASV table)?
sl
what is steam locomotive?
print the first ten lines of a fast file.
I lost access to the server.
What is email Joe?
sed 's/good/bad/g' my_file.txt | 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.
Qiimes two types of file extensions
What is .qza and .qzv?