Hello,

The first input file is not in BED format (specifically, BED12). This would be necessary in order to produce a GFF file with the proper attributes in the feature, frame, and group fields.


The tool BED-to-GFF describes these formats. BED12 files are available from the UCSC table browser and certain other sources. These should not be confused with BED6 files, which are the most common BED format in Galaxy.

Best wishes for your project,

Jen
Galaxy team

On 3/7/12 12:15 AM, Robin Mjelle wrote:
Dear Galaxy

I have a problem converting Interval to GFF.

I used the tool BED-to-GFF
<http://main.g2.bx.psu.edu/tool_runner?tool_id=bed2gff1> converter.
My Interval file contains 18 coulmns:

*chr1   33308998        33309020        +       cel-let-7-5p    0       chr1    
33308999        255     22M     *       0       0       AGAGGAAGAAGGAAGAAAAGAA  
UGAGGUAGUAGGUUGUAUAGUU  XA:i:0  MD:Z:22 NM:i:0*

However my GFF output only contains 9, and it has removed the feature
"*cel-let-7-5p":*

chr1    bed2gff region_0        33308999        33309020        0       +       
.       region_0;



Instead of region_0 I want the gene name, in this case the miRNA name.
How do I do this?

Best Robin


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