Extracting subject sequence in tblastn results
I ran a tblastn search (query=protein, subject=nucleotide database). In the results, the subject start column is greater than the subject end column (since it is mapping to the reverse complement on the subject so this makes sense):
sstart ssend 7130 6200
However if i want to extract the nucleotide sequence from the subject which is mapping to my query, can I just use the following coordinates in bold below? or would this be the incorrect way of extracting my region of interest?
samtools faidx database.fa contig1:6200-7130
Thanks for the input!
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