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Question: Conversion GFF(3) to BED
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gravatar for yasaman.rezvani66
9 months ago by
yasaman.rezvani66 • 0
yasaman.rezvani66 • 0 wrote:

I am uploading a gff file for Toxoplasma Tgondii (GT1) organism on galaxy and try to convert this gff file to bed. But I am not able to choose the data to pass it to the tool and get the bed file out put.

I would appreciate if you could help me with this proble.

I am looking forward to hear back from you, Best Regards, Yasaman Rezvani
gff convert bed gff3 datatype • 940 views
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by yasaman.rezvani66 • 0
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gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The input dataset is not in GFF format and it is not assigned that datatype. Both are required for this conversion tool.

The data appear to be in GFF3 format with a problem in the header and comment lines (those starting with ##). There are tabs included in these lines, instead of the space character, which causes the file to not be autodetected as GFF3. The first line is the most important as it identifies the datatype and should be retained. The other comment lines can be corrected or removed entirely.

FAQs: https://galaxyproject.org/support/#getting-inputs-right

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson ♦ 25k
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