Running alignment using Bowtie by setting specific maximum number of mismatches

Question

[jahanshahi.amin]

Hi everyone, 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?

Regards.

Answer 1

[Pierre Lindenbaum]

filter on NM using samtools ? How to extract alignments with 0 mismatch from sam or bam file by using samtools?

[jahanshahi.amin]

I don't have a sam or bam file! the file format is fasta.

[Pierre Lindenbaum]

but bowtie generates a sam/bam file; use samtools to filter downstream bowtie.

[jahanshahi.amin]

The file which I'm running alignment on it, is fasta. does bowtie support fasta files as input?