Hi,

I am the author for "fml_gff3togtf" tool package, currently merged into our
instance at
http://galaxy.cbio.mskcc.org, The tool can be accessed with following link:
https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed

--/Vipin
Sloan-Kettering Institute
 <http://galaxy.cbio.mskcc.org>

On Mon, Nov 11, 2013 at 12:15 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:

>  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-Jacksonhttp://galaxyproject.org
>
>
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