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Old 06-11-2015, 09:47 AM   #20
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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BBTools has is a pair of programs for cutting (and outputting to a file) the sequence between primer pairs, but not for cutting out primers themselves. Is that what you are after?

The usage is like this:

Assume your set of primers for one end is AAAAAA and AAAAAT, and for the other end is GGGGGG and GGGCCC:

msa.sh in=amplicons.fq out=primer1.sam literal=AAAAAA,AAAAAT
msa.sh in=amplicons.fq out=primer2.sam literal=GGGGGG,GGGCCC


That will find the optimal alignment for the optimal primer, and output one line per amplicon (twice). Then run this:

cutprimers.sh in=amplicons.fq out=middle.fq sam1=primer1.sam sam2=primer2.sam

"middle.fq" will contain the sequence between the primers, one per amplicon, using the best alignment. I designed this to cut V4 regions from full-length 16s.

Notes: msa.sh stands for MultiStateAligner, not for Multiple Sequence Alignment. All sequences can be in any orientation (forward or reverse complement).

Please let me know if that doesn't address your question; I may have misunderstood it.
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