Convertion to gff3 format

Question

[micro32uvas]

Hi everyone,

I have this data about mirna, including its name, accession id, start and end of both hairpin and mature mirna, its sequence and +/- strand in tab delimited format in gedit/notepad++

I want to convert it into gff3 format. can anyone help?

Answer 1

[michael.ante]

Hi micro32uvas,

please have a look at the gff3 specifications (e.g. here). You can use command-line commands like awk to pick the columns of your file in the correct order. Alternatively, you can use Galaxy and click to "Text Manipulation->Cut columns from a table".

Denote, that some programs produces 0-based positions, which need to be converted for gff3 (1-based).

Cheers,

Michael