The remaining unique reads were mapped to snRNAs, snoRNAs, and scRNAs, while miRNAs were found in low frequencies in all test samples.
Our examination of sequencing reads mapped to known snRNA loci revealed very few additional reads with mismatches (Supporting Information, Table S1), suggesting that even if other variants exist, their expression is low and does not affect the calculated relative expression level of known snRNA isoforms.
One of these potential candidates ("hsa-bcm-miR-49") fulfilled all the criteria for the candidates at the high confidence level, and also mapped to a known snRNA.
RNA-seq reads were mapped to the curated snRNA genes using bowtie, allowing no mismatches.
In addition, the presence of structural genes (like 5S rRNA, U1 snRNA and U2 snRNA) mapped to the neo-Y chromosome of E. minor and Dichromatos species would prevent the complete degeneration and loss of these chromosomes (X0 reversion).
The 2'-O-methylation and pseudouridylation sites of human rRNAs and snRNAs were mapped to the chicken rRNA and snRNA sequences.
Unique reads mapped to rice tRNA, rRNA, snRNA, snoRNAs [ 58], known miRNAs [ 59] and TIGR Oryza Repeat Database [ 60] were removed.
Reads mapped to rice tRNA, rRNA, snRNA, snoRNA obtained from fRNAdb (http://www.ncrna.org/frnadb/), NONCODE, GtRNAdb (http://lowelab.ucsc.edu/GtRNAdb/Osati/), and Rfam (ftp://ftp.sanger.ac.uk/pub/databases/Rfam/11.0/) were also removed.
Approximately 3.29% (747,350) of the clean reads could be mapped to known noncoding RNAs (rRNA, snRNA, snoRNA, tRNA) deposited in the NCBI.
Furthermore, a priority rule was applied to ensure that every unique small ncRNA was mapped to only one annotation: tRNAs, rRNAs, snRNAs, snoRNAs, scRNAs > miRNAs > repeats > exons > introns.
