This is a test version of Biostars. For the public version, visit https://www.biostars.org.
convert .fasta to .gft fomat

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
• 2,500 views • link
updated by Juke34 Juke34 • written by mike mike

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

• 0 views • link
written by WouterDeCoster WouterDeCoster

2 answers

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.

• 0 views • link
written by Juke34 Juke34

Log in to answer this question.

More posts like this