I have been extracting genomic sequences, using "Extract genomic DNA" from "Fetch Alignments/Sequences". I used gff files that I have downloaded from NCBI-clone, in a fasta file of a genome assembly, which I have also downloaded from NCBI and uploaded to Galaxy, as the last version of the assembly of that genome is not available to work in Galaxy right now.
According to the example, the names of the sequences in the output fasta file should contain the name of the chromosome/scaffold in the gff file. In my output, the names of the chromosomes/scaffolds in the output fasta file are NOT present in the gff file I used for the extraction. How is that possible? Am I missing something? I am not sure on how the extraction works, then.