How to extract reads from a particular gene from a metagenome
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3.2 years ago
Biok • 0

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!

next-gen assembly gene sequence • 1.2k views
Entering edit mode
2.6 years ago
somnja • 0

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


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