Credit: Darren Baker
Researchers say they’ve developed a computational method that dramatically speeds up estimates of gene activity from RNA sequencing (RNA-seq) data.
With the new method, called Sailfish, estimates of gene expression that previously took hours can be completed in a few minutes.
And the researchers say the accuracy of Sailfish equals or exceeds that of previous methods.
The team described the Sailfish method in Nature Biotechnology.
They noted that gigantic repositories of RNA-seq data now exist, making it possible to re-analyze experiments in light of new discoveries.
“But 15 hours a pop really starts to add up, particularly if you want to look at 100 experiments,” said study author Carl Kingsford, PhD, of Carnegie Mellon University in Pittsburg, Pennsylvania.
“With Sailfish, we can give researchers everything they got from previous methods, but faster.”
With previous methods, the RNA molecules from which read sequences originated could be identified and measured only by mapping the reads to their original positions in the larger molecules—a time-consuming process.
Dr Kingsford and his colleagues found this step can actually be eliminated. The team discovered they could allocate parts of the reads to different types of RNA molecules, much as if each read acted as several “votes” for one molecule or another.
Without the mapping step, Sailfish can complete its RNA analysis 20 to 30 times faster than previous methods.
Dr Kingsford also said the Sailfish method is more robust than previous methods. It’s better able to tolerate errors in the reads or differences between individuals’ genomes.
These errors can prevent some reads from being mapped, he explained. But the Sailfish method can make use of all the RNA read “votes,” which improves the method’s accuracy.
For more information and to download the Sailfish code, visit: http://www.cs.cmu.edu/~ckingsf/software/sailfish/.
