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I'd like to know if there is a simple way to check the concordance between a GTF file and a fasta file (that I use as mapping reference) ?

It may be a dumb question, but I suspect discrepancies between my 2 files and I don't want to check this manually

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  • $\begingroup$ Answer to this specific question --> turn back to the person who provided me the GTF and complain ! :P $\endgroup$
    – elielink
    Aug 11, 2021 at 12:49

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Answer from @ATpoint, converted from comment:

Check whether chromosome identifiers are the same and both files contain the same chromosomes. You can also check that the end coordinate of the GTF never exceeds the length of the respective chromosome. Maybe you can also check whether the first three nucleotides of every CDS indeed start with a start codon. If this is all true then I guess I would trust this pair.

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You might use agat_sq_filter_feature_from_fasta.pl from AGAT

 DESCRIPTION 
 This script is a kind of annotation filter by sequence name. It goes through the gff annotation features and remove those
 that are not linked to a sequence from the fasta file provided. The
 match between sequence name in the fasta file and the 1st column of
 the gff3 file is case sensitive.
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