I am working on WGBS for strawberry (Fragaria vesca) genome. I want to annotate CpG,CHG and CHH islands in the genome. The recent version of the genome has a transcript gff3 file and a genes gff3 file. I am using the methylkit to annotate differentially methylated bases /regions and methylkit requires a bed file for annotation.I have converted the transcript gff3 file to bed.However, I am not able to convert the genes.gff3 file to a bed because the file lacks the first line.When i cheched the file using gff3 validator, it shows that the file lacks the first line denoted as " ##gff-version 3". My questions are:
- How can I insert the line" ##gff-version 3" in the gff3 file.
- Can anyone help calrify if any of the above mentioned gff3 files contain information about CpG, CHH and CHG features? if not.
- Where can I get a gff3 file or bed file that can be used for annotating CpG,CHG and CHH.
I appreciate your help.