How can I know that the blast hits of my NGS data mapping against my query sequence?

Question

[apl00028]

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.

[ATpoint]

May I ask why you use blast instead of a dedicated NGS aligner? Maybe there is a better way of achieving your analysis goal.

[apl00028]

Yeah, I though that It could be useful make an aligment with Bowtie2. But I do not what paramether shows that my hits mapping in an equitative way with my query sequence using Bowtie2

[ATpoint]

Can you give a representative example what exactly you want to see. Blast is going to take a very long time for an entire NGS run.

[apl00028]

I would like to know that the positive hits of my NGS data mapping in more than one position, I mean that it covers a long position of my query sequence