I am facing a technical issue in miRNA. I want to retrieve the sequences of 500 duck miRNAs from ENSEMBLE database using their coordinates. For example I have a miRNA genomic location named as "KB7423821145970_145992", and I want to retrieve the sequence and the name of this miRNAs. Note: duck genome on ensemble are arranged as scaffolds starts with KB. I think two ways exist:
To download a fasta file from ensemble containing the coordinates and sequences, and then I can use R to subset this.
To download a gff3 file containing the coordinates and the names of duck miRNAs or at least sncRNAs, then knowing the names of miRNAs or their transcripts, one can match these with a fasta file being downloaded contains names and sequences , then one can get the sequences ? Any advice ? Any R script that can enable this ?