TAMALPAIS Mark Bieda
TAMALPAIS KNOWN LIMITATION:
1. The first field of the gff file must be by chromosome; in particular, it probably needs to be like chr1
or like chr1, chrX, chrY, chr20.
I suspect (but am not sure) that anything of the form chr(anything) will work. But I am not sure of this. Note that use of non-standard chr names do have the limitation that the optional secondary analyses like location and gene finding would not work.
Non-standard name examples:
Like chr99 might be ok. Or chrMYGOODONE.
What am I talking about?
If you look at the first lines of your gff, you will see in the first column the location designation. For most gffs, this is like chr1. To see examples, go to the sample data page on the website. You will see that these files are by chr.
To look at your own gff files, it is easy to load them into a text editor in Linux, or for windows, I strongly suggest that you use the excellent Notepad++ (do a google search, it is completely free).