Hi everyone,
I'm relatively new to bioinformatics, and I am trying to use some deep amplicon sequencing data from the MiSeq to validate somatic mutations identified from either WES or other targeted sequencing methods.
In terms of experimental design, I have 3 amplicons tiled over each of the mosaic variants in question (range from 3% - 22% AAF) and an average sequencing depth of 10,000X/amplicon using 22 cycles of initial PCR & 8 cycles of indexing with Q5 polymerase.
I'm having trouble identifying the right tools to analyze this kind of data, since I am using unpaired samples and all of the reads will have the same start/end site, preventing me from being able to collapse the reads. Any suggestions? I've combed through pre-existing threads without much luck.
I'm relatively new to bioinformatics, and I am trying to use some deep amplicon sequencing data from the MiSeq to validate somatic mutations identified from either WES or other targeted sequencing methods.
In terms of experimental design, I have 3 amplicons tiled over each of the mosaic variants in question (range from 3% - 22% AAF) and an average sequencing depth of 10,000X/amplicon using 22 cycles of initial PCR & 8 cycles of indexing with Q5 polymerase.
I'm having trouble identifying the right tools to analyze this kind of data, since I am using unpaired samples and all of the reads will have the same start/end site, preventing me from being able to collapse the reads. Any suggestions? I've combed through pre-existing threads without much luck.
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