Training Course on Fusion transcript detection

Tutorial jaffa program

Analisys using JAFFA.

Tutorial with Data

First of all we need to connect with the virtual machine. To achieve this we need to use terminal (if you use linux) or PUtty or mobaxterm

Connect with the virtual machine:

  		**ssh -X nomeutente49@m49.lsb.biocomp.unibo.it**
X11 forwarding request failed on channel 0
Linux m49.lsb.biocomp.unibo.it 4.9.0-3-amd64 #1 SMP Debian 4.9.30-2+deb9u3 (2017-08-06) x86_64

The programs included with the Debian GNU/Linux system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.

Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent
permitted by applicable law.
Last login: Mon Sep  4 10:10:54 2017 from 172.16.197.254
um49@m49:~$

Then we move on the directory of the tutorial

**cd fusion/tutorial-fusion-transcript-2017/**
um49@m49:~/fusion/tutorial-fusion-transcript-2017$

then we aply ls -ltr on the directory:

**(root) um49@m49:~/fusion/tutorial-fusion-transcript-2017$ ls**
RAW  README.md  Results  scripts

On the RAW/ we have the fastq, script contain example script and on Results directory some pre-computed results.

Star the tutorial!!!

Hands On 1

We need to activate the enviroment:

**source /opt/conda/bin/activate**
	(root) um49@m49:~/fusion/tutorial-fusion-transcript-2017$

then we set the directory ot the reference database:

export JAFFA_REF_BASE=/nfs/fusion/JAFFA/

Now we move on directory where we run JAFFA:

cd ~/fusion/tutorial-fusion-transcript-2017/Results/JAFFA/BT4

Now we apply assembly algoritm of jaffa on BT474-demo fastq.:

  
jaffa-assembly ~/fusion/tutorial-fusion-transcript-2017/RAW/BT474-demo_*.fastq.gz

This step require at least 3-5 minutes.

**(root) um49@m49:~/fusion/tutorial-fusion-transcript-2017/Results/JAFFA$ ls**
BT474-demo  checks  commandlog.txt  jaffa_results.csv  jaffa_results.fasta

Two main file we use :

  • jaffa_results.csv
  • jaffa_results.fasta

Look the first 10 lines of the results:

head jaffa_result.csv

with the help of the instruction familiarizate with the output of JAFFA manual

Hands On 2

Please Try to use the other two modules Direct and Hybrid:

cd ..
mkdir  Direct
cd  Direct/
jaffa-Direct ~/fusion/tutorial-fusion-transcript-2017/RAW/BT474-demo_*.fastq.gz 


cd ..
mkdir Hybrid
cd Hybrid

jaffa-hybrid ~/fusion/tutorial-fusion-transcript-2017/RAW/BT474-demo_*.fastq.gz

Hands On 3

How can detect fusion on MCF7-Sample using jaffa?

This step require 4-5 minutes. Move on MCF7 directory and run jaffa-assembly

cd ~/fusion/tutorial-fusion-transcript-2017/Results/JAFFA/MCF7/

jaffa-assembly ~/fusion/tutorial-fusion-transcript-2017/RAW/MCF7-demo_*.fastq.gz

Hands On 4 (Optional)

Run all the samples in the same time. This produce a sigle csv with the name of the samples and fusions.

cd ~/fusion/tutorial-fusion-transcript-2017/Results/JAFFA/
mkdir ALL
rm -rf BT4/ MCF7/
cd ALL/


jaffa-assembly ~/fusion/tutorial-fusion-transcript-2017/RAW/MCF7-demo_*.fastq.gz ~/fusion/tutorial-fusion-transcript-2017/RAW/BT474-demo_*.fastq.gz

Hands On 5 (Optional)

Run all the samples in the same time. Run hybryd protocol for both samples.

cd ~/fusion/tutorial-fusion-transcript-2017/Results/JAFFA/
mkdir Hy_all/
cd Hy_all


jaffa-hybrid  ~/fusion/tutorial-fusion-transcript-2017/RAW/MCF7-demo_*.fastq.gz ~/fusion/tutorial-fusion-transcript-2017/RAW/BT474-demo_*.fastq.gz