2.5. Differential adenylation and non-adenine residue analysis
The FASTQ files were remapped with default –ax map-ont flags to theRiccia fluitans transcriptome, which was created by compilation of stringtie and gffread v.0.12.7 script . The nanopolish v.0.14.1 program (https://github.com/jts/nanopolish) was used to extract tail information for each transcript. Finally, the nanotail v.0.1.0 package (https://github.com/smaegol/nanotail) was applied to run a statistical method based on the general linear model (glm) to determine the significance of any differences in tail length. Transcripts with an adjusted p-value < 0.05 were considered as statistically significant. Previously generated nanopolish outputs, sequencing summary generated by the Guppy bascaller, and fast5 files were used to identify non-adenine (non-A) sites in the poly(A) tail by the ninetails v.1.0.0 program (https://github.com/LRB-IIMCB/ninetails).