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# System prepended metadata

title: Notes from Lab

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# Notes from Lab
Log in

ssh kkhtut24@bi278
Password

Locate relevant files that we are organizing

cd /courses/bi278/Course_Materials/lab_01a

Go home 
	cd ~
Make folders to organization
	mkdir lab_01a lab_01b
Copy files into relevant directory
	cp /courses/bi278/Course_Materials/lab_01a/* ./lab_01a
Enter new folder
	Cd ~/lab_01a
Ensure files are copied over
	Ls
Create organization folders within using
	Mkdir ./foldername
Use
	Mv A B (a being initial file, b being target destination)

Repeat for every file until organized


Exercise 2

In order to read genomic files, navigate to directory with genomic files

Cd /courses/bi278/Course_Materials/lab_01b

Then, use grep command to find individual chromosomes/contigs or genes labeled by > in FASTA

grep ">" /courses/bi278/Course_Materials/lab_01b/filename

In order to count the number of base pairs inside of a genomic file, use the wc command with -c

Wc -c ./filename 

In order to find the GC percent, use grep to first isolate the GCs of the genome, delete the non GC, then do a wc count, piping the results form one command into the next using |

grep -v ">" ./test.fa | tr -d -c GCgc | wc -c

Tr works by taking set1, defined by GCgc, then deletes the complement of GCgc (-d -c)

Once you have a count of GCs, use awk to calculate the percent of GCs to ATGCs

Awk ‘BEGIN {print (253/400)}’

This process can be repeated for each genomic sample in order to evaluate the GC content of dna sequences. 



Commands used:
Cd : change directory, usage is “cd (pathway)” and requires using a complete path file directory
Cp: copy, can copy files form one location to another, usage is “cp (subject filepath) (desired filepath)”
Mkdir: used to make folder directories, usage is mkdir (folder name), makes a folder within current directory
Ls: list, lists items present in current directory or target directories. 
Mv: move, used to move files form one location to another, usage is “mv (subject filepath) (desired filepath)”
Grep: used to find a subject pattern, usage is “gp “pattern”(pattern location)”
Wc: word count, used to count characters or words in a text file, comes with various options that can modify command
Man: manual, used to find various options for any command
Tr: translate, used to translate or delete characters, use man to find options for usage.
awk: used to execute any number of different functions and calculations, use man to find options and usage. 


