How to map amplicon sequences to a reference with masked sequences?

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2.4 years ago

LDT ▴ 340

Dear all,

I have millions of amplicon sequences that I want to map to their reference, which looks like this.


    NNNNNNNNAATTCCTCGAGAAGCTTGGGCCGATGTCCACGAAGCTCTCCTACGNNNNNNNNNNNNNNNNNNNNNNNNNCAGTCCAGCGCCAACCAGATAAGTGAAATCTAGTTCCAAACTATTTTGTCATTTTTAATTTTCGTATTAGCTTACGACGCTACACCNNNNNNNN

The masked sequences with the 25 NNNNNNNNNNNNNNNNNNNNNNNNN in the middle are of great importance for me. So far I have used bwa and bowtie2 and geneious aligner.

Bwa and bowtie2 avoid mapping anything in the 25 NNNNNNNNNNNNNNNNNNNNNNNNN area. Geneious does, though, and the results are as I want them. However, I want to automatise the process and use a command-line aligner because I have hundreds of files.

I need your help.

reference amplicon bwa bowtie2 alignment • 607 views

ADD COMMENT • link updated 13 months ago by corrector ▴ 30 • written 2.4 years ago by LDT ▴ 340