Running alignment using Bowtie by setting specific maximum number of mismatches
I need to run blast process on a sequence file by specifying some special parameters. here are the parameters:
1- word size of 6
2- allowed maximum 2 mismatch (on each side)
I'm using ncbi blast to do the alignment using the following command:
blastn -query seq.fasta -db ref -out results.txt -num_threads 8 -outfmt '6 qseqid sseqid sseq' -word_size 6
Since I couldn't define maximum mismatch for the mentioned command, I decided to use bowtie to do the alignment process.
would you please tell me the bowtie command equivalent to ncbi blast command which I mentioned with considering the maximum allowed number of mismatches?
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