Detecting Viral Integrations Using RNA-Seq

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/* .

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