Genomics of Gene Expression

The Conesa Lab is proud to announce that our collaborative paper from the Long-Read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium has been published in Nature Methods. This consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse, and manatee species.

Developers utilized these data to address challenges in transcript isoform detection, quantification, and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

We are committed to driving innovation and excellence in genomic research. Thank you for your continued support and interest in our work!