Question: How to use a genome assembly file to extract or find the gene or region I am interested in?
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gravatar for guttapaajob
3.8 years ago by
Norway
guttapaajob0 wrote:

Public archived rat genome assembly, FASTA format, although sorted by chromosomes, as can be viewed with IGV program, it looks not annotated. Can I use this genome assembly to compare with to the released rat genome assembly but only focusing on my interested region? I am pretty new with the genome assemblies and deep sequencing datasets, so detailed steps and basic approaches are highly appreciated. :-)

David

sequence assembly genome • 1.8k views
ADD COMMENTlink modified 3.8 years ago by geek_y8.7k • written 3.8 years ago by guttapaajob0

I don't understand very well your question, what are you trying to do? If you want to extract defined region of your genome, you can use Bedtools getfasta  (http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.html). You only need to know the chromosome and coordinates of your region of interest and make manually a bed file. You can extract the region in both genomes and then compare the sequences.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by iraun3.4k

OK, I want to compare the newly sequenced rat assembly with the latest rat assembly Rnor_5.0. But I need only MHC region. I know which chromosome and approximately where on chromosome the MHC region is, but with no annotations, I don't know the structure of the newly sequenced rat strain. That is what I try to find out.

ADD REPLYlink written 3.8 years ago by guttapaajob0
0
gravatar for geek_y
3.8 years ago by
geek_y8.7k
geek_y8.7k wrote:

Extract the MHC region from the annotated genome using bedtools or any script. 

Align the extracted MHC region to newly assembled genome and see if there are any differences like rearrangements.

You could use SyMap for aligning long queries, which inturn runs nucmer, a popular tool for comparing large genomes. SyMap is GUI based and has good visualizations like synteny maps and circos type of plots.

ADD COMMENTlink written 3.8 years ago by geek_y8.7k

Thank you for your perfect suggestion! I will try it out.:-)

ADD REPLYlink written 3.8 years ago by guttapaajob0
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