Sunday, December 18, 2016

This finally happend: novel tool for fusion discovery from RNA-seq data

There was a long and a bit crazy story, however the toolkit that I was working on has now a publication in PLOS OnE. In short, tool has some unique features including support of strand-specificity to detect anti-sense chimeras and discovery of intergenic fusions. It's open-source and available in bitbucket repo.

It took us more than 3 years to finish the publication and this was amazing experience, which allowed me to learn what really can happen in science. Main lesson: there can be serious competition in research area that results in multiple unexpected issues. The journals with high impact factor are complex systems. Imagine submitting a manuscript, waiting for review 4 months(!) and receiving a statement that the "manuscript should be rejected while tool ability X is not important", with some strange citations. And then, exactly one month after rejection of your manuscript, there is a publication in the same journal with main statement of "the importance of ability X" in their tool. In our case the "ability X" was fusion isoform discovery confirmed with experimental validation.

This was probably main project for me during PhD and a perfect lesson. Of course, I am super grateful to my supervisor Dr. Fernando Garcia-Alcalde, to the whole team from MPIIB and to Lexogen company for amazing support. Moreover, additional useful comments I received from Prof. Steven Salzberg and he doesn't need an introduction for those who are working in sequencing data analysis area (btw, there is also his awesome blog).

Despite the complexity and multiple factors, science remains to me the most exciting and interesting area, where critical revision and communication have high impact. I will be glad to any comments, fixes or suggestions about InFusion. And of course, wish everyone not to experience any strange "non-scientific" problems, but have honest and correct reviews. Stay in science ;)