liftover between close species

Question

[tim.ivanov.92]

I have 2 coordinates on the reference genome, and i want to find corresponding nucleotide sequences of this region on a list a close related organisms. What are the best approaches/tools for this job?

Answer 1

[GenoMax]

liftOver (and the chain files that go with it) from UCSC, if you are working with a genome available there. Some additional options mentioned in CrossMap.

[tim.ivanov.92]

but liftOver has this warning

WARNING: liftOver was only designed to work between different assemblies of the same organism. It may not do what you want if you are lifting between different organisms. If there has been a rearrangement in one of the species, the size of the region being mapped may change dramatically after mapping.

[GenoMax]

Yes it does. I think UCSC has done the due diligence while creating the liftover/net files. You can use liftOver and then double check the data by alignment yourself, if you are worried about the warning above.

[tim.ivanov.92]

well, ok thank you :)

is it hard on requirements, though? What is the minimal set of inputs?

[GenoMax]

Since you have only 2 coordinates use web form. From and To selection of genomes (only ones available will be shown). And your coordinate data in BED format. Minimal requirement is in the link on the liftOver page (https://genome.ucsc.edu/FAQ/FAQformat.html#format1 only 3 fields are required).

[tim.ivanov.92]

well, i sort of simplified the bigger task, to get the idea

i will be doing it on multiple organisms (all related, its drosophila family), and on many coordinates

[GenoMax]

Then you would need to use the command line version of the program that you can download (linux only, scroll down on the page). Luckily Drosophila genomes are represented and as long as ones you need are there you should be set. Note: You can only use the tool for genomes that have a chain/net file combination available (which is what provides the mapping). You can make those files yourself if you need to use it on genomes not present there. It would not be trivial.

[tim.ivanov.92]

thank you again, for all your answers

chain files is exactly whats been troubling me. Are you saying, there are cross-pair maps between drosophila species, made by ucsc project? Where can i download them? Or look up

[GenoMax]

See this page. Find the Drosophila genomes. Liftover (chain) files have their own link under each genome. There are multiple genome build for each.