EPP531_Applied Genome Analytics - AlinaPokhrel/Pokhrel-EPP531 GitHub Wiki

Lab 1:05-02-2024

created a new screen named “LAB_1”
```
screen -S LAB_1
```
Created a new directory named “Commandline_Lab”
```
mkdir Commandline_Lab
```
changed into the directory ‘Commandline_Lab’
```
cd Commandline_Lab
```
Checked the content of the directory
```
ls; ls-all; ls -a
```
Created a text file named ‘Text_1.txt’ and wrote ‘welcome to Applied Genome Analytics’ into it
```
nano Text_1.txt
```
welcome to Applied Genome Analytics
control+x, y
Renamed the file ‘Text_1.txt’ to ‘Myfile_1.txt’
```
mv Text_1.txt Myfile_1.txt
```

Exported the file ‘Myfile_1.txt’ from Sphinx to local computer desktop
In a new terminal:

scp [email protected]:/pickett_sphinx/projects/EPP531_AGA/Pokhrel/Commandline_Lab/Myfile_1.txt /Users/alinapokhrel/desktop

Deleted the file ‘Myfile_1.txt’ from server
```
rm Myfile_1.txt
```

Again imported file ‘Myfile_1.txt’ from local desktop to Sphinx

scp ./Myfile_1.txt [email protected]:/pickett_sphinx/projects/EPP531_AGA/Pokhrel/Commandline_Lab

Downloaded a folder named DATA onto the computer

Imported the folder DATA to current working directory i.e. Commandline_Lab

scp –r ./DATA [email protected]:/pickett_sphinx/projects/EPP531_AGA/Pokhrel/Commandline_Lab

Counted the number of files in the folder
```
ls -l | grep "^-" | wc -l 
```
ls ~~l gives detailed information about files; grep "^~~" filters the regular files starting with “-”; wc -l counts the number of lines corresponding to the number of files
Peek into the file named ‘mgGenes.txt’
```
less mgGenes.txt
```
Count the number of genes in the file ‘mgGenes.txt’
```
cat mgGenes.txt|grep "MG"| wc -l ; 525
```
list of first 10 and last 10 lines of ‘mgGenes.txt’
```
head mgGenes.txt
tail mgGenes.txt
```
Count the number of genes on positive strand in ‘mgGenes.txt’
```
cat mgGenes.txt|grep "+"| wc -l
```
299
Count the number of genes on negative strand in ‘mgGenes.txt’
```
cat mgGenes.txt|grep "-"| wc -l 
```
227
compared the number of positive and negative strands to the total number of genes
```
echo "299+227" | bc
```
526
There was a flaw either in counting positive () or negative (-) strands as total number of genes was 525 but summing the positive and negative strands gave 526. The #16 and #17 step counted the number of "" and “-” in whole file, but the strand information is on only on the fourth column. As we peek into the file, we can see that there was a problem in column five of the file ‘mgGenes.txt’.So, to cut the column five to find out if there is any “+” or “-” sign in this column, following code was run:
```
cut -f 5 mgGenes.txt|grep "+"
```
there were no extra “+”
```
cut -f 5 mgGenes.txt|grep "-"
```
rpmG-2 and polC-2
The file ‘mgGenes.txt’ was then edited in nano text editor to correct the flaw
The “+” genes were extracted into a new file called ‘Plus_genes.txt’ excluding the gene names i.e. excluding column 5
```
cut -f 1-4 mgGenes.txt |grep "+" > Plus_genes.txt
```
The “-” genes were extracted into a new file called ‘Minus_genes.txt’ excluding the gene names i.e. excluding column 5
```
cut -f 1-4 mgGenes.txt |grep "-" > Minus_genes.txt
```
To extract line 250 from the file ‘mgGenes.txt’
```
head -n 250 mgGenes.txt|tail -n1
```
MG_228 274653 275135 + dhfR

EPP531_Applied Genome Analytics - AlinaPokhrel/Pokhrel-EPP531 GitHub Wiki

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