Hello,
There are no tools directly on the public Galaxy site to transform a
GFF3 dataset into a BED12 dataset. However, the Tool Shed has a
repository called ' fml_gff3togtf' that includes a tool for this
purpose, for use in a local install. The description is a bit bothersome
in that it a slightly incorrect datatype statement, so be sure to test
out the results. (the word "wiggle" has no place in this statement: "
gff3_to_bed_converter.py: This tool converts gene transcript annotation from GFF3 format to UCSC wiggle 12 column BED format.")
http://getgalaxy.org
http://usegalaxy.org/toolshed
I see your post at Biostar, and it might be helpful to let you know what
a BED12 file represents (plus I'll post this there, may help others):
http://www.biostars.org/p/85869/
A BED12 file describes the complete, often spliced, alignment of a
sequence to a reference genome. This does not include minor base
variation, it is a macro alignment. You can think of each of the blocks
as being "exons", although there is no magic here - if the sequence or
genome had quality problems, or significant variation (large insertion
or deletion), that could cause the alignment to fragment as well.
Here is the data description:
http://wiki.galaxyproject.org/Learn/Datatypes#Bed
To see examples, at UCSC (genome.ucsc.edu), EST or mRNA track will have
this as the primary table format. All gene track can also be in BED12
format, or in a related one, genePred:
http://genome.ucsc.edu/FAQ/FAQformat.html#format9
UCSC also has line-command utilities to convert between the formats,
pre-compiled versions are here:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads
Either way, you can convert the data, then load up into the public
Galaxy (usegalaxy.org) and proceed with your analysis. BEDTools works
well with BED12 files. There is definitely information loss attempting
to transform BED6 -> BED12, as the global alignment is lost. And
adjusting attributes such as score or name are often a preference, so
you can alter these however you want, as long as the attribute
formatting rules for the columns are followed.
Hopefully this helps,
Jen
Galaxy team
On 11/9/13 3:29 PM, lrutter @iastate.edu wrote:
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 , ,
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--
Jennifer Hillman-Jackson
http://galaxyproject.org
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