ncRNA-Seq processing error

So i have this data set of non coding RNA seq data i humans, but when i head it, i can see the sequences with Thymine base pair and not Uracil base pair, am i missing something or is the file problematic. I am using this tool Meta2OM and Nmix to predict the 2' methylation sites in RNA seqs. They take fasta files, so i converted my fastq into fasta with sed commands and then am planning to replace the T s with U s. Anybody who did ncRNA seq please do share your opinion.