Calculating relative abundance of taxonomies from BLAST output

Question

[Ming]

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.

[Asaf]

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.

Answer 1

[5heikki]

how to extract best hits of blast in terms of e-value, identity,...?