Possible Gene Unflattening Error In Bp_Genbank2Gff3.Pl Bioperl Script

Question

[Panos]

I want gff3 files for certain Vertebrates, but I could only find the corresponding genbank files in Ensembl. So I decided to download them and convert them to gff3, using the bioperl script bp_genbank2gff3. Even though it produces a gff3 file, I get an error and I'm not sure if the resulting file is okay to use... More specifically, the most frequent message I get is a "Possible gene unflattening error".

I have used bp_genbank2gff3 a few times so far, but it's the first time I'm seeing that kind of error. What I find weird is that, even though it says it encountered an error, it produces a gff file...

If you want to reproduce the error, get the following genbank file

wget ftp://ftp.ensembl.org/pub/release-73/genbank/gallus_gallus/Gallus_gallus.Galgal4.73.chromosome.10.dat.gz

and try to convert it using

bp_genkbank2gff3 Gallus_gallus.Galgal4.73.chromosome.10.dat.gz

For your information, I have also tried first decompressing the gzipped file and then running bp_genbank2gff3, but I still get the same error.

Has anyone else seen this error? If so, how do you fix it?

Thanks, Panos

Answer 1

[Emily]

Hi Panos

I don't know about the bp_genbank2gff3 script, but if you can't get it to work, then a workaround would be to download the GTF files from Ensembl, then convert these to GFF3.

Emily

[Panos]

Thanks for the advice Emily! Why is gtf2gff3 outputting an unsorted gff file, though? Does it, at least, keep the features of a gene (like CDSs, exons, etc) right after each gene?

[Emily]

I'm afraid I'm not totally familiar with the script. The README only shows the example of a single gene so it's not clear. You could test it on two genes and see what it does with them.