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!
1 answer
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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