Question: convert .fasta to .gft fomat
2
gravatar for mike
2.4 years ago by
mike60
Germany
mike60 wrote:

I have denovo assemblies from cufflinks in .gtf format and assemblies from Trinity in .fasta format. I want to merge both assemblies. How can I convert fasta to .gft format?

Thanks

assembly • 878 views
ADD COMMENTlink modified 2.4 years ago by Juke-342.1k • written 2.4 years ago by mike60

Are you sure that what you are doing is biologically meaningful? What's the aim of doing this?

ADD REPLYlink written 2.4 years ago by WouterDeCoster38k
0
gravatar for dago
2.4 years ago by
dago2.5k
Germany
dago2.5k wrote:

Few links that might help:

http://seqanswers.com/forums/showthread.php?t=44455

https://biostar.usegalaxy.org/p/1835/

http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html

ADD COMMENTlink written 2.4 years ago by dago2.5k
0
gravatar for Juke-34
2.4 years ago by
Juke-342.1k
Sweden
Juke-342.1k wrote:

You have to map your fasta on your genome using a splice aware aligner like exonerate or scipio. The aligners give you most of time as output either gtf or gff files. If it is gff it will be easy to convert it in gtf.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Juke-342.1k
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