How to edit a mapped genome?

Question

[lizabe]

Hi everyone!! I am mapping contigs against a reference genome, i used Contiguator and Mauve and with both tools i am getting mapped at first position the rpmH gene and then dnaA gene despite in my reference genome dnaA is at first position and rpmH is at the end of the genome. How can edit or change this mapping?? Thanks!!

[GenoMax]

If the reference genome is correct then it can only mean that your contig must be incorrect. Those two genes must have been switched in the contig. So you could edit that contig to match the reference.

Answer 1

[harold.smith.tarheel]

If your genome is circular, then the observed behavior is expected (i.e., rpmH is physically adjacent to dnaA, so the contig is correct).

[GenoMax]

Presumably there are additional genes besides the two in the contig that can be used to decide if the order of the genes in the contig is right otherwise I am not able to visualize why the genome being circular would make order of the genes on the contig correct.

[harold.smith.tarheel]

The OP said that dnaA is at the start of the genome (I assume that's what was meant by first position) and rpmH at the end, but that the two genes are adjacent on the contig. Both of those observations are consistent if the genome is circular but represented linearly.

Answer 2

[lizabe]

Thanks to everyone! I will try editing the contigs and running the order the contigs tool in Mauve again. And yes, the genomes are from Acinetobacter so they are circular.