Tools for downstream analysis of SAM/BAM files generated using STAR to find Fusion genes

[Dibyendu Dutta]

Hi,

I am trying to analyze my Human cancer RNA-Seq data from Illumina HiSeq to identify Fusion genes. I am very new to this and after reading through various tools, chose to use Bowtie2 and STAR to try out aligning the data using it.

After browsing through most of the Fusion gene finder tools like deFuse and SOAPfuse it seems like all of them are automated pipelines which want to carry out all the processing directly from the beginning taking the FastQ files as input and running bowtie or BWA to align again, which I have already done.

I wanted to know if there exists such tools that I could feed the STAR generated SAM/BAM for downstream analysis to find fusion genes.

[Alexander Dobin]

Hi Dibyendu,

at the moment I am not aware of any tool that would automatically process STAR's chimeric output.

Some discussion about it is in this post.

In principle, it should be relatively straightforward.

Cheers

Alex

[Simon White]

The chimera package in Bioconductor can read the Chimeric.out.junction files and processes it to look for fusion transcripts.

[Raghu Prasad Rao Metpally]

Hi Simon,

Did you tried Chimera? and sucess with it?
I tried chimera never had sucess with it?

Can you ouline your steps

thanks
Raghu

[Simon White]

We are in the process of testing it out, i will let you know how we get on.

Simon

[Johnbosco Tayebwa]

I am also interested in finding out how chimera works for you!

[andrea....@gmail.com]

Hi, 

you can also use FusionSeq (https://github.com/sbonerlab/fusionseq for the most recent version). The tool can use the output from STAR to identify fusion genes.

Best,

Andrea

On Wednesday, July 10, 2013 2:59:28 PM UTC-4, Dibyendu Dutta wrote:

[Johnbosco Tayebwa]

Hi,

I used git clone to get fusionseq and was hoping to install it with ./configure, make, make install as per the instructions in the INSTALL file. However, there is no such file apart from configure.ac. What is the simplest way to install fusionseq? I have CentOS.

[Vladan Arsenijevic]

Hi all,

I was following this topic and have a few updates. First, there is a tool that can be easily used for additional analysis on fusion transcripts, Onconfuse, http://www.unav.es/genetica/oncofuse.html. It accepts Chimeric.out.junction as an input. Alex, it would be nice to have your comment here. Further, I cannot recommend FusionSeq for this task, found it painful to set it to work, and it's not straightforward to convert Chimeric.out.sam to mrf format (a function sam2mrf is buggy), a unique format FusionSeq can deal with.

Cheers,
Vladan