Thank you. Do you familiar with python package that I can integrate into a pipeline?
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Alignment with deletion
Hello,
I have a DNA sequence with some deletions. I have a reference sequence, with deletions as well.
I want to align these reads pairwise.
However, when I'm using Align packages (or others), it considers the deletions as mismatches:
Is there a method to count deletions as matches if performed in both sequences?
Thank you!
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1 answer
You can use EMBOSS Needle for DNA:
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How will the information be carried over if you are doing pairwise alignments? e.g. how would the aligner know to put a gap in the sequences if it is simply aligning the two sequences you show in the example above.