Tentative project for microRNA identification with online-available genomes of birds
First, create conda environment named "mirbird"
conda create -name mirbird
source activate mirbird
Second, download required software packages and update existing packages.
Two major software package used are:
NCBI Genome Downloading Scripts https://github.com/kblin/ncbi-genome-download
MirMachine https://github.com/sinanugur/MirMachine
conda install -c bioconda ncbi-genome-download
conda install mirmachine -c bioconda -c conda-forge
From Genbank, we can select bird genomes with good quality to cover most of the bird families.
The script loops across selected bird species. For each species, the script:
- Downloads and unzips the genome from Genbank.
- Identify possible microRNA from the genome using MirMachine.
- Extracts the results and deletes the genome and intermidiate files.