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       ,       ,