Aligning Draft to Reference genomes, rearranging contigs?
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4.0 years ago
YOUSEUFS ▴ 20

Hello Bioinformagicians!

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:

ref x-axis, draft y-axis

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?

Many thanks!

P.S I hope the image link works!

mummer Assembly alignment • 1.6k views
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Why would the order of your contigs matter in the context of your end goal?

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I don't know to be honest, I'm just checking from more experienced people than myself to see if it would =)

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Maybe if you were scaffolding your contigs, and assuming that it worked, then the number of mapped reads could increase a little bit (assuming your assembly is good otherwise). IRL, scaffolding without long mate pairs or other such data is pointless though..

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