text: user12767: 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
  
  user73: 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.
  
original_text: 12767: <p>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) ?</p>
  <p>It may be a dumb question, but I suspect discrepancies between my 2 files and I don't want to check this manually</p>
   73: <p><em>Answer from @ATpoint, converted from comment:</em></p>
  <p>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.</p>
  