I am new to analysis of RNA sequencing data. I am looking to map small RNA sequencing data with a gff3 file I downloaded from miRBase. Now, I need to convert the .gff3 file to gtf file for usage in mapping tools. I went through the Biostars looking for older posts but I still could not understand how to properly convert the .gff3 file and I am still confused on the filters that the tool has, for the conversion of .gff3 file to gtf file. Can anyone please guide me on the usage of gffread tool in Galaxy?
The tool will transform GFF3 to GTF format using all default parameters with the exception of the option "Feature File Output". Choose GTF and supply a track name (a single alphanumeric "word" is best).
If you need more help to better understand a specific parameter, which one?