Question: How can I compare two reference genome
0
gravatar for yasmint
12 months ago by
yasmint0
yasmint0 wrote:

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 • 547 views
ADD COMMENTlink modified 12 months ago by Antonio R. Franco4.5k • written 12 months ago by yasmint0
  1. Make a list of genes from annotations, unique to each assembly
  2. Intersect the differentially expressed gene list with these two lists.
ADD REPLYlink modified 12 months ago • written 12 months ago by cpad011213k
1
gravatar for colindaven
12 months ago by
colindaven2.2k
Hannover Medical School
colindaven2.2k wrote:

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

ADD COMMENTlink written 12 months ago by colindaven2.2k
1
gravatar for Antonio R. Franco
12 months ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

Give a try to programs like Mauve

ADD COMMENTlink written 12 months ago by Antonio R. Franco4.5k
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