I used the following code to do blastx (by last version of ncbi-blast+) of my transcriptome assembly against the proteome reference,
blastx -query file1 -db pr_database -out file1_1.out -e-value 1e-3 -max_target_seqs 20 -outfmt 6
Now, I have two questions; given my command, are all blast hit is the best or I look at also other parameters, like identity and alignment length?. Sharing your factors to select the best hit would be highly appreciated.
Also, could you please provide me how to extract desired hit in terms of e-value and identity or alignment length (if it is necessary)?