Relaxed alignment using Bowtie
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23 months ago
seqalign • 0

I have NextSeq 1x75 bp sequencing data that I'm trying to align using relaxed settings. My goal is to allow alignments with up to 4% mismatches. To do this, I have come up with the following command in bowtie:

bowtie -S -p 16 -n 3 -l 75 ref reads.fastq out.sam


With these settings I believe that I am allowing for 3 mismatches per 75 bp, or per read, resulting in up to 4% mismatches. Is what I believe is happening congruent with what is actually happening?

bowtie alignment • 371 views
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Your calculation is right for 4 %. You must be knowing the default seed length ( -l ) is 28. But if give it 75, Reads of smaller length will be not be mapped (I think). Since your read chemistry is 1*75 and u must carry trimming and many of your read lengths would have become shorter due to quality and adapters. So I would suggest not to give a higher seed length.

I would suggest you check read length distribution of data after trimming.