Question: converting .gff file to .gtf
0
gravatar for kudzu
17 months ago by
kudzu0
United States
kudzu0 wrote:

I am trying to upload annotation file to the galaxy rna seq work flow, but i have annotation in the .gff format, what is the easiest way to convert .gff file to .gtf file

rna-seq • 2.3k views
ADD COMMENTlink modified 17 months ago by Jeffin Rockey1.1k • written 17 months ago by kudzu0
1

Refer this

ADD REPLYlink written 17 months ago by Chirag Parsania1.7k

Have you tried to search converting .gff file to .gtf? I got several hits, from BioStars, SeqAnswers, ResearchGate... For example, gffread is cited very often, you could give it a try.

ADD REPLYlink written 17 months ago by h.mon28k
3
gravatar for Jeffin Rockey
17 months ago by
Jeffin Rockey1.1k
Karimannoor
Jeffin Rockey1.1k wrote:

Few other programs that do the conversion.

genome tools

http://genometools.org/tools/gt_gff3_to_gtf.html

ea-utils

https://github.com/ExpressionAnalysis/ea-utils/blob/master/clipper/gff2gtf

pasa

https://github.com/PASApipeline/PASApipeline/blob/master/misc_utilities/gff3_to_gtf_format.pl

kent utils:

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

gff3ToGenePred followed by genePredToGtf

GFFtools-GX

https://github.com/vipints/GFFtools-GX/blob/master/gff_to_gtf.py

ADD COMMENTlink modified 17 months ago • written 17 months ago by Jeffin Rockey1.1k
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