Generate GTF file

Question

[daewowo]

Is there a tool that can generate a GTF from a fasta file -eg GCF_000001405.39_GRCh38.p13_genomic.fna?

I can convert the fasta to bed, and know that BEDOPS can convert GFF to BED, but I want to go the other way.

Either GFF or GTF is fine as there are tools to convert GFF to GTF

Ultimately I am just trying to get full genome level (not chomosome level detail) statistics on mapping depth and coverage from a bam file when doing multi genome alignment, and qualimap2 map be able to give me summary details per genome if I have the GTF file for each genome.

Answer 1

[GenoMax]

You can get a GTF file for this genome by going to this NCBI link. Click on the Download button about half way down the page and then select a GTF file to download as option.

[daewowo]

How can I generate a GTF file if NCBI doesnt have it?

[GenoMax]

You will first need to identify genes using a gene prediction/annotation program. Then use gene model information to create the GTF file. Fasta files only have sequence and you can't generate a GTF file using simple sequence.

[colindaven]

Another way, given you have a genome and a set of transcripts in FASTA format, is to use the excellent gmap tool with gff3 output to map the transcripts. Then convert gff3 to gtf format using many different tools.