Question: Reference Covering Issue Using Amplicon Reads
gravatar for Sam
7.5 years ago by
United States
Sam10 wrote:

I got HBV amplicon reads from a patient, and want to reconstruct HBV quasispecies using a reference and the amplicon reads. When I aligned them to a given reference(3320 bp long) I noticed that the reads are not covering the entire reference. the tool I am using can't handle gaps. In such case , what people do?

next-gen sequencing • 1.2k views
ADD COMMENTlink modified 5.9 years ago by Biostar ♦♦ 20 • written 7.5 years ago by Sam10

Hi Sam, can you give us more information about what tool you are using for alignment?

ADD REPLYlink written 7.4 years ago by Alex Paciorkowski3.3k
gravatar for Ram
7.4 years ago by
Ram0 wrote:

If your have Sff format of your input file...try using Amplicon Variant Analyzer (AVA).

ADD COMMENTlink written 7.4 years ago by Ram0
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