1. Data Preparation
a. Create a directory named ‘viral’ in your home directory and change to the ‘viral’ directory
mkdir viral cd viral
b. Link the input files, the perl scripts and a template config file to your ‘viral’ directory
ln -s ~/Desktop/rnaseq_a/input/vfs/* . ls
2. Find Viral Integrations
a. Look at the contents of the input files
b. Run the viral integration search using the below command;
perl viral.fusion.pl config vfs.conf insertSIZE 350 HKCI5a_gz CL7R_1_VFS.fq.gz CL7R_2_VFS.fq.gz
c. Look at the results file