Hi Everyone,

I’ve got an amplicon that has fixed and variable sequence segments, and Im sequencing it with 180 base MiSeq reads.  I’d like to align the reads using the fixed segment.  Is this an appropriate job for either Bowtie or BWA (using a reference sequence that is necessarily shorter than the reads) ?  If not, how should I do it ?

Thanks,

Seth

Seth Stern, Ph.D.

sethster@comcast.net

650 996 8726 (cell)