Difference between perc_identity and qcov_hsp_perc in blastn
I'm following the manual of software where sequences are blasted against each other to create a match-list that is later passed to R, the code is:
blastn -db OTU_sequences.fasta -outfmt '6 qseqid sseqid pident' -out match_list.txt -qcov_hsp_perc 80 -perc_identity 84 -query OTU_sequences.fasta
What I cannot understand here is: what is the difference between the perc_identity and qcov_hsp_perc parameters?
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