Question: How to extract reads from a particular gene from a metagenome
gravatar for Biok
12 months ago by
Biok0 wrote:

Hi everyone,

I have a very basic question, I have metagenomic samples and I want to extract reads from a particular gene (amoA gene) to see the diversity of this gene between samples but I am not sure what would be the best approach. Should I just blast the metagenomic reads against amoA sequences? or maybe it is better to assemble first and then blast and extract the sequences?

Thank you for your time!

sequence next-gen assembly gene • 385 views
ADD COMMENTlink modified 5 months ago by somnja0 • written 12 months ago by Biok0
gravatar for somnja
5 months ago by
somnja0 wrote:

Hey, i don'have an answer for you, but am having the same problem currently. I want to extract specific reads from specific genes from an unassembled metagenome. Did you find an answer yet? So far i am thinking of either using blast with a small database of reference sequences of that gene, or mapping the reads to reference sequences

ADD COMMENTlink written 5 months ago by somnja0
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