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