Protein abundance-Metagenomes
I would greatly appreciate your assistance with a task I am currently working on. I have approximately 300 metagenomes and am trying to quantify the abundance of specific proteins (using the raw reads from the metagenomes). Could a DIAMOND-based approach be effective in this case? I am new to this field, so any guidance would be helpful.
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Are you planning to search with
DIAMONDagainst a set of specific proteins or something more generic likeswissprot/nr? Depending on the protein you are looking at (and the domains etc that may be shared with other unrelated proteins) the results you get may need to be carefully parsed. But in terms of getting the job done quicker thanblast+, this should work. Provided you have the necessary hardware.