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Showing the original subject when running BLAST
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4.4 years ago
kdsilva • 0

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.

Entering edit mode

You can always look-up the entire sequence using the subject identifier. BLAST is local alignment, it doesn't concern itself with entire sequences.


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