Hi everyone, I'm running blast nucleotide with word-size of 6 using the following command:
blastn -query 6452.fasta -db ref -out BlastResults.txt -num_threads 8 -outfmt '6 qseqid sseqid sseq' -word_size 6
Now I want to set the number of mismatch to 2 for the command. how should I add it? I added "-penalty 2" to command but it doesn't work!