Problem: When names of a GFF3 and a FASTA don't match, then downstream tools will run, but not reference the input fasta file to 'extract' features of the length called for by the gff3 file.
Solution: Change the names to match. Use the Rename tool for both GFF3 and FASTA files, or the FASTA sequence renamer tool
jrr-cpt
commented
4 years ago
Symptom: GFF3 feature extraction tool output has all ???? of correct length for genes
Problem: When names of a GFF3 and a FASTA don't match, then downstream tools will run, but not reference the input fasta file to 'extract' features of the length called for by the gff3 file.
Solution: Change the names to match. Use the Rename tool for both GFF3 and FASTA files, or the FASTA sequence renamer tool