Hi all,
I have a set of SNPs for an organism for which annotation is still in progress. I obtained set of SNPs of interest and to get functional information I have GFF file with genes predicted by Augustus and GFF3 file with proteins annotation from InterProScan. Is there any tool that would let me integrate this information or will I be forced to write my own script? I didn't manage to find what I need so far but maybe I'm missing something.
So far I annotated my SNPs with augustus GFF file using snpEff but I can't do the same with InterProScan GFF3 file as I am having more or less this kind of output of building database for my organism:
Reading GFF3 data file : 'path_to_file' Total: 0 markers added.
Create exons from CDS (if needed):
Exons created for 0 transcripts.
Deleting redundant exons (if needed):
Total transcripts with deleted exons: 0
Collapsing zero length introns (if needed):
Total collapsed transcripts: 0
Reading sequences :
Reading FASTA file: 'path_to_reference'
Reading sequence 'scf_1', length: 2205567
Adding genomic sequences to exons: Done (0 sequences added, 0 ignored).
Reading sequence 'scf_2', length: 1244474
Adding genomic sequences to exons: Done (0 sequences added, 0 ignored).
Reading sequence 'scf_3', length: 1199189
Adding genomic sequences to exons: Done (0 sequences added, 0 ignored).
Reading sequence 'scf_4', length: 3287760
Adding genomic sequences to exons: Done (0 sequences added, 0 ignored).
And later on:
Total: 0 sequences added, 0 sequences ignored.
Adjusting transcripts:
Adjusting genes:
Adjusting chromosomes lengths:
Ranking exons:
Create UTRs from CDS (if needed):
Correcting exons based on frame information.
Remove empty chromosomes:
Removing empty chromosome: 'g4789.t1'
Removing empty chromosome: 'g7757.t1'
Removing empty chromosome: 'g5919.t1'
It's the same for all scaffolds and genes - it looks to me like my genes are treated as chromosomes. How could I use this GFF3 file to biuld snpEff database for the annotation?
Regards, Agata
