Question: How do I find the same gene in two different assemblies?
gravatar for jstevenson2256
17 months ago by
jstevenson225610 wrote:

I have two genome assemblies from two phenotypes of a non-model ant species. I have performed gene prediction on them both and have found a difference in the number of predicted genes. How do I find these differing genes? I can't compare gene IDs as they will be different in both assemblies and I can't pull their positions and compare them as the same gene has different coordinates in both assemblies simply due to the assemblies being different.

Any ideas on how I can compare these putative genes between the two genomes?

ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 17 months ago by jstevenson225610

Maybe blast can help?

ADD REPLYlink written 17 months ago by Benn8.0k

For non coding genes, UTRs etc it would also be good to generate a chain file for liftOver (provided only assemblies are different and species are same/very_similar) . I have used this pipe line with good results to generate chain files which then can be used by crossmap/liftOver to convert coordinates.

ADD REPLYlink written 17 months ago by microfuge1.8k

I also think generating your own chain files and use liftOver is a good shoot. Otherwise, extract the genomic sequence of each gene and then use blat or gmap to map the to the other assembly.

ADD REPLYlink written 16 months ago by Geparada1.4k
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