miRNA annotation
The miRNA annotation files used in ncPRO-seq are created based on files from miRBase [8]. The precursor miRNA gff file downloaded from miRBase can be used in ncPRO-seq after being transformed from gff2 to gff3 format. In miRBase, we cannot find genome coordinates of mature miRNAs. Therefore, we wrote a custom script to generate mature miRNA annotation file based on the mature miRNA sequences, precursor miRNA sequences and precursor miRNA annotation file.
Example of "attributes" column in precursor miRNA annotation file:
ACC=MI0006363;ID=hsa-mir-1302-2
Example of "attributes" column in mature miRNA annotation file:
Name=mmu-miR-206*;Precursor=mmu-mir-206;ID=mmu.miR.206star
Nicolas Servant
2012-05-31
