Comparison of software for fusion genes

[Khanjan]

Hi there,

There are several algorithms for fusion gene detection floating around. You guys have an idea which one works the best for Illumina HiSeq PE data?

Or any suggestion, on which one to use for cancer data ?


Thanks a lot !
K

[Nicolas]

Hi,

I had good results (ie. found the fusion known to be present in a cell line) with chimerascan: http://code.google.com/p/chimerascan/

For me, the main advantage on the other softwares is simply that it worked! Most others were impossible to install or crashing after hours of computation. That might be entirely my fault. I would be very interested to hear better and more informed feedback on the various options.

[jujubix]

deFuse maybe?

http://compbio.bccrc.ca/software/defuse/

It was tested on Illumina GAII paired end tumour data, which seems to fit your needs?

[ndaniel]

FusionCatcher for finding gene fusions in RNA-seq data is very easy to use and has found tens of novel fusion genes which have been validated using RT-PCR!

http://code.google.com/p/fusioncatcher/

[jp.]

Hi
can someone tell me how get fusion-break-point in chimerascan ? it gives only two spanning reads, but not the exact break-point. Whereas, deFuse and tophat-fusion give exact break-point seq.
does anyboy has answer ?
thank you

Hi,

I had good results (ie. found the fusion known to be present in a cell line) with chimerascan: http://code.google.com/p/chimerascan/

For me, the main advantage on the other softwares is simply that it worked! Most others were impossible to install or crashing after hours of computation. That might be entirely my fault. I would be very interested to hear better and more informed feedback on the various options.

[ndaniel]

Hi there,

There are several algorithms for fusion gene detection floating around. You guys have an idea which one works the best for Illumina HiSeq PE data?

Or any suggestion, on which one to use for cancer data ?


Thanks a lot !
K

Here is an extensive comparison of fusion genes finders using real RNA-seq data:

https://code.google.com/p/fusioncatcher/wiki/comparison

[Bukowski]

FusionCatcher for finding gene fusions in RNA-seq data is very easy to use and has found tens of novel fusion genes which have been validated using RT-PCR!

http://code.google.com/p/fusioncatcher/

We use FusionCatcher, and have been for some time, and are very happy with its performance. We've been using it on cancer samples and its been good for picking out known fusions in characterised lines as well as fusions that have validated subsequently.

[fafnir1990]

It is possible to use fasta contigs as fusioncatcher input?

[ndaniel]

It is possible to use fasta contigs as fusioncatcher input?

It depends how long are those contig sequences and how many of those are there.

If one converts the FASTA files into FASTQ files (e.g. https://code.google.com/p/fasta-to-fastq/ , https://www.biostars.org/p/99886/ ) then virtually all the fusion finders should be able to take them as input.