Question

gff3 to gtf

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8.5 years ago

luanabarbos • 0

Hi guys,

I need to convert a gff3 file to gtf to use at tophat. I tried to convert using the gffread ( came with Cufflinks), but it didn't work. Could anyone help me with this?

next-gen gff gtf • 4.0k views

ADD COMMENT • link updated 7.4 years ago by grant.hovhannisyan ★ 2.6k • written 8.5 years ago by luanabarbos • 0

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Which species is this data in GFF3 format for? I wonder if a GTF is not already available out there...

ADD REPLY • link 8.5 years ago by Denise CS ★ 5.2k

score 0 · Answer 1 · 2016-05-31

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8.5 years ago

Jean-Karim Heriche 27k

Have a look at this older post. There also seems to be a Galaxy tool for this.

ADD COMMENT • link 8.5 years ago by Jean-Karim Heriche 27k

score 0 · Answer 2 · 2017-07-22

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7.4 years ago

grant.hovhannisyan ★ 2.6k

Gffread utility from Cufflinks is what you need. What was your command line for it that did not work?

ADD COMMENT • link 7.4 years ago by grant.hovhannisyan ★ 2.6k