Question regarding retrieving miRNA sequences from ENSEMBLE
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Last seen 4.1 years ago

Dear all,

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:

  1. To download a fasta file from ensemble containing the coordinates and sequences, and then I can use R to subset this.

  2. 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 ?

ensembl • 624 views
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It’s not appropriate to add “deseq2” tag to this. Note that when you do this it actually sends emails to package developers.


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