Convert whole genome mRNA file from NCBI to gff file.

Question

[nish_laa]

I have extracted the whole genome sequence from NCBI. Now I have to create the gff file for each gene in the genome. is there any online tools available ?

[GenoMax]

Now I have to create the gff file for each gene in the genome

I doubt you want to do that. You probably want to make a single GTF/GFF file for the entire genome.

I have extracted the whole genome sequence from NCBI.

What does this mean? Did you download the genome sequence from NCBI? Then it is likely that NCBI already has a GTF/GFF file available. What genome did you download, provide accession number.

[Ram]

A? What kind of meaningless tag is that? Please put some effort into your post, and at the least do not make things a mockery.

Answer 1

[sam]

Hi Nish,

Here I assume that the GFF file is not available in NCBI. GFF files are available for many genomes in NCBI. At the same time, many have only genome data but not GFF files. See this link https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/907/166/925/GCA_907166925.1_wheat_cv_fielder_v1_assembly/.

To prepare an annotation file for your genome, you could do it as follows:

1. use marker software: To do this, you should have the following:

     a. Bulk RNA data mapped against your genome.
   
     b. repeat sequence data (prepared using repeat-masker).  
   
     c. Collect reviewed protein sequences from closely related genomes.
   

2. Use Liftoff: If you have a well-annotated genome closely related to your genome of interest, you could lift over the annotation from a previously annotated reference genome to your genome of interest.

3. If you have bulk RNA data for your genome, you could use StringTie or Trinity to make a GFF file

I hope this helps.

Good luck!