Question: A way to verify that GFF and Fasta files make a valid pair (came from the same project version)
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gravatar for Denis
12 weeks ago by
Denis30
Denis30 wrote:

Sorry for the weird question. I have GFF and Fasta files. I'm looking for the way to check if they relate to the same project version, i.e. in the GFF file i have correct annotation for the sequences in Fasta file. Is it realistic task?

assembly genome • 177 views
ADD COMMENTlink written 12 weeks ago by Denis30
2

I think it is easy to spot if a fasta / gff pair are not compatible (different chromosome names, features outside chromosome ranges). However, there is no guarantee the gff and fasta they are from the same project if you don't find incompatibilities.

ADD REPLYlink written 12 weeks ago by h.mon21k
2

One additional note: You'll make your and your colleagues life easier in the future if you include the sequence part in the gff directly. Any gff can contain an arbitrary sized sequence section after a ##FASTA directive See other syntax section in the gff specification

ADD REPLYlink written 12 weeks ago by Carambakaracho570
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