Analyze Amplicon Seq results for variants and mutation sites
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Sara • 0
@41d09ed8
Last seen 10 weeks ago
United States

Hello,

I have several Paired-End, Amplicon Sequenced data. The amplicon is 222 base-pairs and 2x250 sequencing was done so there is heavy overlap. I already aligned these sequences to the reference amplicon using BWA and created weblogos to display any regions with mutations.

I would like to do more analysis including:

  • Get fraction of mutated alignments versus wildtype

  • Display all of the different variants and their fraction within the pool of reads.

I can't find information online to tackle this issue. I would like to make an allele frequency table, listing all of the variant sequences and displaying the mutations- similar to the output table made when using Crispresso2 but these are not CRISPR-edited sequences. I am not sure if I am using the correct vocabulary and that is why I can't find the solutions that I am searching for.

I created VCF files from the bam files and am trying to investigate what I can do with these.

Any guidance would be appreciated. Thank You, Sara

virus pcr amplican mutations • 428 views
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