But now i have a another question for giff to bed function.
i want to use gff-to-bed function after i run it, it seems that i got the results :
Info: 0 lines converted to BED. Skipped 74166 blank/comment/invalid lines starting with line #1.
i am using gff3 file.and it is the first few lines.
##genome-build MSU Rice Genome Annotation Project osa1r6
##species Oryza sativa spp japonica cv Nipponbare
##sequence-region Chr1 1 43268879
Chr1 MSU_osa1r6 gene 1903 9817 . + . ID=13101.t00001;Name=TBC%20domain%20containing%20protein%2C%20expressed;Alias=LOC_Os01g01010
Chr1 MSU_osa1r6 mRNA 1903 9817 . + . ID=13101.m00001;Parent=13101.t00001;Alias=LOC_Os01g01010.1
Chr1 MSU_osa1r6 five_prime_UTR 1903 2268 . + . Parent=13101.m00001
Chr1 MSU_osa1r6 five_prime_UTR 2354 2448 . + . Parent=13101.m00001
This appears to be a valid GFF3 file and should work fine. We'll look into this and get back to you.
There was a bug in our GFF-to-BED converter that was causing this problem. It's been fixed in galaxy-central changeset 4554:3ea6ee14a8b7 and will be available on our public server next time it is updated.