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).