Our RNA research team, consisting of group members at the FU/RKI, supported by the Smyth team at HZI (Würzburg)/CNRS(Strasbourg) developed a fast, reliable and cost-saving method for barcoding and demultiplexing direct-RNA (dRNA) sequencing data generated by Oxford Nanopore Technology (ONT) sequencing devices, paving the way for more sophisticated experimental designs for epitranscriptome research (link to paper).
During nanopore sequencing, individual (DNA or DNA/RNA hybrid) molecules are threaded through a protein (nano-) pore that is embedded in an electrically resistant polymer membrane. The translocation of the molecules generates characteristic time-series of electrical current. For dRNA-sequencing a DNA adaptor is required, which contains a customizable barcode (RTA barcode). Normally, the raw electrical signal is translated by basecallers (large machine learning models) into respective RNA or DNA sequence. However, RNA basecallers cannot basecall DNA sequence and hence the RTA barcode.
To overcome this bottleneck and provide a low-cost solution for barcoding, we developed WarpDemuX, a tool that foremost suggests RTA barcodes that are distinguishable in raw signal space and subsequently is able to detect and distinguish the different barcodes.
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