I have been having challenges converting my gff3 file generated strawberry genome (Fragaria vesca) to a bed12 format which is required for annotating differentially methylated bases. I have read through several solutions offered but have not found the one that works for my data. However, I have come across a github script (https://github.com/pzross/iver/blob/master/R/bioinfo.R) which requires that I download gfftogenepred and genepredtobed12 tools from UCSC and run the scripts in R program inorder to generate the bed12 format. At the point of generating a gfftogenepred file, I get the following error message:
/tmp/tmp.gff:0: empty GFF file, must have header /tmp/tmp.gff:0: invalid GFF3 header GFF3: 2 parser errors
My GFF3 file looks fine (with 9 columns)
Please I need help.
Thank you in advance