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How do I find the same gene in two different assemblies?

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?

rna-seq assembly alignment genome
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updated by Biostar Biostar • written by jstevenson2256 • jstevenson2256

Maybe blast can help?

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written by Benn Benn

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 https://github.com/wurmlab/flo with good results to generate chain files which then can be used by crossmap/liftOver to convert coordinates.

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written by microfuge microfuge

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.

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written by Geparada Geparada

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