Calculating relative abundance of taxonomies from BLAST output
Dear All,
I am trying to calculate the relative abundance of taxonomies derived from a BLAST output. I have observed that one predicted gen/qseqid has multiple matches to the subject/sseqid. This will affect the relative abundance as the relative abundance will get inflated. How do I select the best subject/sseqid (maybe in terms of the best bitscore) from the BLAST output?
Will appreciate any input. Thank you.
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If there is more than one good hit you might want to assign a higher taxonomic level that combines the results. There are many tools to determine taxonomic profiles, I can't think of a reason to use BLAST for that task.