Bioinformatics Seminars

Bioinformatics Seminar

Time: 11AM
Venue: Zoom Webinar

1 March 2022

This is a 3rd year PhD Seminar

Benchmarking long-read RNA-seq analysis tools using in silico mixtures

Xueyi Dong
WEHI Epigenetics and Development

The growing popularity of long-read sequencing technology in transcriptomic studies has led to the development of customised algorithms for isoform identification and workflows for differential expression analysis. However, the current lack of benchmark datasets with inbuilt ground-truth makes it challenging to compare the performance of the different methods available. Here, we generated a benchmark experiment using two human lung adenocarcinoma cell lines that were each profiled in triplicate together along with synthetic, spliced, spike-in RNAs (sequins). These samples were deeply sequenced on both Illumina short-read and Oxford Nanopore Technology long-read platforms. Alongside the ground truth available via the sequins spike-ins, we created in silico mixture samples by combining reads from the pure RNA samples in known proportions to allow performance assessment in the absence of true positives or true negatives. Using these data, we compared six isoform detection tools, five differential transcript expression (DTE) tools and five differential transcript usage (DTU) tools. In this seminar, I will present results from this benchmarking analysis and provide some guidance on method choice for different analysis tasks.

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