Converting Fasta To Gtf

Question

[tscheitel]

Hi,

is there a way to convert a fasta file to gtf?

thanks

Tomas

Answer 1

[Damian Kao]

Fasta files give the user sequence data. GTF files give the user coordinate data among other things. They differ by data content, not simply formatting. Unless your fasta file has extra data in the headers that you can use to create a GTF file, there is no straightforward way to convert fasta to GTF.

The other option is to to map your sequences to whatever reference sequence you want and then make a GTF file from the mapping.

[PoGibas]

As Damian Kao said: OP can map sequences and make a GTF.
Here are some suggestions:

• Blat to GFF (perl);
• PSL to GFF (CGAT);
• PSL to GFF (using Galaxy) (from seqanswer.com).

[JulianC]

Hi Damian!

Could you tell me how to make a GTF file from mapped reads? Thanks!