Showing the original subject when running BLAST
I'm running the following command:
blastn -query references.fasta -subject reads.fasta -task blastn-short -outfmt "6" -out output.csv
I would like to see the ENTIRE subject sequence in the output. Is there a way to do this? It looks like including "sseq" in the outfmt shows me the aligned part of the subject sequence, but I'd like to see the entire thing.
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You can always look-up the entire sequence using the subject identifier. BLAST is local alignment, it doesn't concern itself with entire sequences.