Extract transcript fasta sequences using gtf

Question

[otieno43]

Hello, I am trying to extract fasta sequences of transcripts in genome fasta file with gtf annotation file using gffread that used the command: gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf. However, when I execute this, I get 0k of trranscript.fasta (empty). I am unable to figure out what could be the problem. Anyone who can help please.

Here is the command I used and the results:

./gffread/gffread -w transcripts.fasta -g /Users/ee/Desktop/genome/VectorBase-56_GfuscipesIAEA2018_Genome.fasta /Users/ee/Desktop/genome/Gfus_x10_vNew.gtf

Results
290K VectorBase-56_GfuscipesIAEA2018_Genome.fasta
0B transcripts.fa
2.1K gclib

Thanks Erick

[rpolicastro]

Are the fasta and gtf obtained from the same source? You may want to include a link to them. It's important that the gtf corresponds to the correct assembly, and that formatting such as chromosome names are the same.

[Juke34]

On top of the important checks mentioned by rpolicastro you can check what type of feature is present in the gff file ( You need transcript feature for that command to work). You may use agat_sp_extract_sequences.pl from AGAT that will list at the beginning of the parsing log, the feature types found in your file.

[otieno43]

The gtf file has transcript feature in it.

[otieno43]

Yes the fasta and gtf files are from the same source. The gtf features correspond correctly with the genome assembly. Everything seems correct, I can't just figure out what is the issue. I can share with you the gtf and genome fasta file.

[rpolicastro]

Yea, please share the files and I can check them.