I did a blastn of my NGS sequences against a NCBI database, following the next steps:
firstly make a database: makeblastdb -in hk_db.fasta -title "HK" -dbtype nucl -out hk_db -parse_seqids
then, I did the blast analysis: blastn -query PV001_1_trim.fa -db hk_db -evalue 1e-4 -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen qcovs" -out PV001_1_blast.out
I got the results and I analyzed by R. I got the number of hits that match among my query sequence and my NGS data, I would like to know if there is some way to know if these hits mapping along the query sequence or not.
Thanks in advance.