My end goal is to map some RNA-seq data to a genome iv'e been given but I do not know if this genome is assembled in the right order. In order to analyse this, I'm attempting to align a draft genome sequence (containing contigs and scaffolds) to a closely related reference genome using nucmer. When I plot the output.delta file using mummerplot I get this graph:
The genomes seem to align very well except that they are shifted slightly with the initial missing piece appearing to the right of the plot. I'm assuming that the start of the sequences of each genome is different, does this matter if I'm to compare the genome? Do they need to start at the same sequence? If so how do I go about rearranging this genome?
P.S I hope the image link works!