How to map amplicon sequences to a reference with masked sequences?
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.
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LDT •
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Minimap should work well for you