MinION sequencing
FAST5 files were base-called to generate FASTQ files using Guppy (version 6.1.7), and this fastQ Library was mapped (using minimap2) to a concatenated genome combining HVS-BAC sequence and Marmoset (Callithrix Jacchus) genome. The output BAM files were used alongside the FASTQ and FAST5 data as inputs to nanopolish v0.14 to determine poly(A) tail lengths.
RNA was extracted from OMK cells 48 hours after infection at MOI 2500 genomes per cell, using TRIZOL with two additional 70% ethanol washes, and stored as an ethanol pellet at -80 C until library preparation. PolyA-based library preparation was performed with the RNA002 kit (Oxford Nanopore Technologies) including reverse transcription with Induro reverse transcriptase(NEB), followed immediately by direct RNA sequencing using a MIN106D version R9.4.1 flow cell.