Hi all,

I have a customed database and I used it to BLASTn against a bacterial genome. **I would like to extract the unmatched regions only.**

Is there a command line or another way to do it?

Thanks very much for your precious help!
1. output in outfmt 6
2. convert to BED/GTF/GFF
3. `bedtools complement`
3. `bedtools getfasta`