# 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.