Hello Jennifer:

Thank you so much for the descriptions, and for sharing the method to check
that the difference in line count is appropriate.

Sincerely,
Lindsay Rutter


On Tue, Nov 12, 2013 at 7:09 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:

>  Hi Lindsay,
>
> Nice to hear that Vipin's server worked out for you.
>
> A reduction in the number of lines is completely expected. You should have
> the same number of lines in the BED12 file as you have unique "ID"s in the
> GFF3 file, if you want to double check. This is the same as the number of
> unique transcripts in any of the files, if summed up correctly.
>
> Why is this? A GFF3 file has one line per feature. Part of an exon, etc.
> with further (this can vary) annotation that tells you if it is 5' UTR, or
> CDS, etc. When converting GFF3 -> BED12, all the features for a particular
> transcript are rolled up into a single line of output. Transcripts will
> have a unique "ID" by GFF3 specification - and all features that belong to
> that transcript will have it in the GFF3 file's attributes field (it is
> usually the first attribute listed).
>
> When you converted just GFF3 -> BED6, each feature was individually
> converted into a distinct line of BED formatted output, there was no
> summing up to group the information for the transcript as a whole.
>
> The Galaxy wiki has more - GFF3 can represent other kinds of data, and
> that is covered in the link-outs to the original spec, but this is the gist
> of the meaning for your specific data.
>
> Glad I could help before, and that Vipin had the tool online & available
> to simplify things!
>
> Best,
>
> Jen
> Galaxy team
>
>
> On 11/12/13 4:12 PM, Lindsay Rutter wrote:
>
> Hello Jennifer:
>
>  Thank you for your very helpful and detailed explanation!
>
>  I ended up using the site that Vipin provided in his message (
> https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed).
>
>  Indeed, it produced a file with 12 columns that appears to be in a
> reasonable bed format (including the 10th column being an integer, with the
> 11th and 12th column consisting of that integer number of items separated
> by commas).
>
>  However, I noticed that the number of lines in the file went
> from 183,748 (in the .gff3 file) to 11,506 (in the 12-column .bed file).
>
>  In your opinion, does this seem like a reasonable reduction in number of
> lines? I was not expecting that (in fact, I was expecting the number of
> lines would stay the same, as they did going from .gff3 to 6-column .bed
> file), but I am quite inexperienced using these files.
>
>  Thanking you...
> Lindsay
>
>
>
>
> On Mon, Nov 11, 2013 at 11:15 AM, 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
>>
>>
>
> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>
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