Question: How can I compare two reference genome
0
gravatar for yasmint
7 days 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 • 128 views
ADD COMMENTlink modified 6 days ago by Antonio R. Franco4.0k • written 7 days 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 7 days ago • written 7 days ago by cpad011211k
1
gravatar for colindaven
6 days ago by
colindaven1.2k
Hannover Medical School
colindaven1.2k 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 6 days ago by colindaven1.2k
1
gravatar for Antonio R. Franco
6 days ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

Give a try to programs like Mauve

ADD COMMENTlink written 6 days ago by Antonio R. Franco4.0k
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