Hello Galaxy:

I am trying overall to convert a .gff3 file to 12-column .bed file.

I first tried GFF-to-BED converter, but it gave a 6-column .bed file.

Then, I tried BED-to-bigBed converter by inputting the 6-column .bed file. I get an error "Unspecified genome build, click the pencil icon in the history item to set the genome build".

So, I click the pencil icon, and see 4 tabs at the top. I set the "Attributes" tab as in the attached image (Attributes.png).

But then, when I select "Convert Format", I am only seeing an option that outputs .bed12 file as "Convert Genomic Intervals to Strict BED12". I am a bit confused about this because I specified the input file as a .bed file (and not genomic intervals, unless I am misunderstanding something).

In any case, when I select "Convert Genomic Intervals to Strict BED12", I do get a .bed file with 12 columns. But I would like to ask if I may have lost information going from the .gff3 to .bed(6) to .bed(12)?

(I feel that scores were all set to "0" from .gff3 to .bed(6), and columns 10, 11, 12 (block counts, sizes, and starting positions) were all set to zero going from .bed(6) to .bed(12)).

If I am correct that there is information loss, is there a system in Galaxy to prevent this, and transfer as much information as possible from .gff3 to .bed(12)?

Thank you. L. Rutter

** Below is a head of my three files (the species is P. dominula):

.gff3 file

##gff-version 3 ##date Mon Nov 4 14:54:42 2013 ##source gbrowse gbgff gff3 dumper PdomScaf0001 maker gene 15 1963 . - . Name=PdomGene00025;ID=1;Dbxref=MAKER:maker-PdomScaf0001-snap-gene-0.274 PdomScaf0001 maker mRNA 15 1963 . - . Name=PdomMRNA00025.1;Parent=1;ID=2;_QI=216%7C0%7C0.2%7C0.6%7C0.5%7C0.6%7C5%7C0%7C98;_eAED=0.43;_AED=0.43;Dbxref=MAKER:maker-PdomScaf0001-snap-gene-0.274-mRNA-1 PdomScaf0001 maker exon 15 100 -0.094 - . Parent=2;ID=3 PdomScaf0001 maker CDS 15 100 . - 2 Parent=2;ID=4 PdomScaf0001 maker exon 223 300 21.8 - . Parent=2;ID=5 PdomScaf0001 maker CDS 223 300 . - 2 Parent=2;ID=6 PdomScaf0001 maker exon 717 765 22.4 - . Parent=2;ID=7

.bed(6) file

PdomScaf0001 14 1963 gene 0 - PdomScaf0001 14 1963 mRNA 0 - PdomScaf0001 14 100 exon 0 - PdomScaf0001 14 100 CDS 0 - PdomScaf0001 222 300 exon 0 - PdomScaf0001 222 300 CDS 0 - PdomScaf0001 716 765 exon 0 - PdomScaf0001 716 765 CDS 0 - PdomScaf0001 906 947 exon 0 - PdomScaf0001 906 947 CDS 0 -

.bed(12) file

PdomScaf0001 14 1963 gene 0 - 14 1963 0 0 , , PdomScaf0001 14 1963 mRNA 0 - 14 1963 0 0 , , PdomScaf0001 14 100 exon 0 - 14 100 0 0 , , PdomScaf0001 14 100 CDS 0 - 14 100 0 0 , , PdomScaf0001 222 300 exon 0 - 222 300 0 0 , , PdomScaf0001 222 300 CDS 0 - 222 300 0 0 , , PdomScaf0001 716 765 exon 0 - 716 765 0 0 , , PdomScaf0001 716 765 CDS 0 - 716 765 0 0 , , PdomScaf0001 906 947 exon 0 - 906 947 0 0 , , PdomScaf0001 906 947 CDS 0 - 906 947 0 0 , ,