ISTOCK, EGALWhen Lior Pachter came across one of the latest publications from the federally funded Genotype-Tissue Expression (GTEx) project, he couldn’t suppress his disappointment.
In the paper, published last October, researchers from the GTEx consortium had analyzed RNA sequencing (RNA-seq) data from more than 40 tissue types in the human body. The findings themselves were exciting, says Pachter, a computational biologist at Caltech. But a single line, tucked away in the methods section, left him feeling exasperated. The line read: “RNA-seq reads were aligned to the human genome . . . using TopHat (v1.4).”
In response, Pachter took to Twitter. “Please stop using Tophat,” he wrote in early December. “There is no reason to use it anymore.”
TopHat version 1.4 was a 2012 update to an open-source program conceived by Pachter and his colleagues in 2008 that aligns reads from RNA-seq experiments to a reference genome. Not only is ...
