I used the Extract Genomic DNA function in Galaxy and it outputted a fasta file using my original genome fasta and my annotation. However, in each entry of the multifasta file, the sequences are duplicated twice.
If you notice, "TATATTTATTAATTTACGGGATC" is duplicated twice in the single entry. This happens to all of genes in the fasta file. When looking at the coordinates, the number of nucleotides does not add up because the sequence is duplicated within it and is twice the supposed size according to the coordinates. For example, coordinates of 700 - 750 should have 50 nucleotides but in my fasta file it has 100.
I have run this function in galaxy twice and I still have this problem. I am sure that my annotation has the correct coordinates and that there is nothing wrong with the genome as it works for all of my other functions. Thanks for the help!