Hi
I’ve run Maker with a fasta genome (581 scaffolds, 5 chromosomes and 576 unplaced).
Maker succesfully annotated my genome with ncbi ESTs and swissprot proteins.
However I was not cappable to train Augustus and, among other things I’ve re-run maker with a modified fasta file where I shortened names (removed all after first withespace) and set lines to 100 bp (normalizd genome) and removed lowercases (awk text reformatting)
Now I only get a single chromosome annotated
Can you tell me what i’m doing wrong?
Thank you