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How can I compare two reference genome

Hi everyone,

I am working on gonadal transcriptimes in lamprey. Two reference genomes are available for the species. There are differences in the number of genes in two assemblies but the annotations are poor. I want to find out which genes are expressed in my sample but missing in one of the genomes. How can I do that? I would really appreciate your suggestions.

Thanks, Tamanna

rna-seq assembly genome
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updated by Antonio R. Franco Antonio R. Franco • written by yasmint • yasmint
  1. Make a list of genes from annotations, unique to each assembly
  2. Intersect the differentially expressed gene list with these two lists.
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written by cpad0112 cpad0112

2 answers

I like to do this kind of analysis on sequence level, as it likely more robust than the annotations

You can

You can also include identifiers from a closely related species if one exists

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written by colindaven colindaven

Give a try to programs like Mauve

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written by Antonio R. Franco Antonio R. Franco

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