convert .fasta to .gft fomat

Question

[mike]

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

[WouterDeCoster]

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

Answer 1

[dago]

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

Answer 2

[Juke34]

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.