If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
Workflow for artificial reporter amplicon analysis
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?