Hi,
I would like to sequence a 1kb region from a genome I am currently assembling. My current 800Mb assembly has around 9000 scaffolds and is far from being finished but I have to compare two different individuals to see whether they come from different populations.
So I thought it would be enough to just Sanger sequence a random 1kb part and hope to see a difference between them (unless I hit a really conserved region). I've never constructed primers myself for anything but as far as I've seen most online/offline software works on "short" sequences rather than chromosomes or entire genomes.
How should I go about this and which primer designing software should I use? Would just blasting primers do the job?
Thx!
I would like to sequence a 1kb region from a genome I am currently assembling. My current 800Mb assembly has around 9000 scaffolds and is far from being finished but I have to compare two different individuals to see whether they come from different populations.
So I thought it would be enough to just Sanger sequence a random 1kb part and hope to see a difference between them (unless I hit a really conserved region). I've never constructed primers myself for anything but as far as I've seen most online/offline software works on "short" sequences rather than chromosomes or entire genomes.
How should I go about this and which primer designing software should I use? Would just blasting primers do the job?
Thx!
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