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Workflow for artificial reporter amplicon analysis

polalphapolalpha Seattle, WAMember

We are working on a project of sequencing of an artificial reporter from human cell line using miSeq (2x300bp). We used PCR method to obtain the amplicons (with UMIs).
We are currently stuck at the analysis stage. Unfortunately I don't have much background in bioinformatics, but just overall ideas about what I'm looking for. The sequencing support where I sequenced my samples are not familiar with this type of analysis. The person who is helping me was able to get the filtered sequences, and align with reference using BWA. Then we have no idea how to do the proper analysis and variant calling.
Can anyone provide a workflow about this type of analysis and redirect us to the right track?
Thank you!

Issue · Github
by Sheila

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