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Polyadenylation Site Usage Analysis Using RNA-Seq

1. Example Data Set

a. Create a directory - dapars - in your home directory and change to that directory

mkdir dapars

 

b. Copy the test dataset folder to your dapars folder

cp /usr/local/bioinf/dapars/DaPars_Test_Dataset.zip dapars

 

c. Change directory to your dapars folder and make sure you have the .zip file

cd dapars
ls

 

d. Unzip the test directory folder

unzip DaPars_Test_Dataset.zip

 

e. Change directory to the unzipped folder - DaPars_Test_Dataset and look what we have there

cd DaPars_Test_Dataset
ls

2. DaPars Configuration

DaPars requires a configuration file to run. The configuration file has everything DaPars need. DaPars needs two sample files (RNA-Seq alignment data and the gene model). Look at the contents of the wig files, UTR file, refseq id file, gene bed file.

a. Open the “DaPars_test_data_configure.txt” in text editor, set the output directory line like below;

Output_directory=results

3. Run DaPars

...using the below command;

python /usr/local/bin/DaPars_main.py DaPars_test_data_configure.txt

4. Scripting the run

Lets write a script to automate steps 1 to 8.

a. Open the text editor from Applications, Accessories, gedit or pluma 

b. Turn on the highlight mode, by choosing; View - Highlight mode - sh

c. Type the below commands (these are the ones that you typed from 1 to 3 above);

mkdir daparscripted
cp /usr/local/bioinf/dapars/DaPars_Test_Dataset.zip daparscripted
cd daparscripted
unzip DaPars_Test_Dataset.zip
cd DaPars_Test_Dataset
mv DaPars_Test_data DaPars_Test_data_old
#this line is a comment about the below line - the below line runs dapars
python /usr/local/bin/DaPars_main.py DaPars_test_data_configure.txt
echo "Congratulations on creating and successfully running your script/program/software"

 

d. Save the file, with the name ‘daparscripted’

e. In the terminal, navigate to the folder where you save the script and run the script with the following command;

./daparscripted.sh

 

f. Make the script executable, using the below command;

chmod 755 daparscripted.sh
ls -lh

 

g. Now run the script as done in #4e above and see if your script worked.