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.
Jumping libraries are created to bypass difficult to align/map regions, such as those containing repetitive DNA sequences. Briefly, the DNA of interest is identified, cut into fragments either with restriction enzymes or by shearing. The size-selected fragments are ligated to adapters for bead-capture and circularized. After bead-capture, the DNA is linearized via restriction enzymes, and can be sequenced using adapter primers facing in outward [reverse/forward (RF)] directions. These library inserts are considered jumping because the ends originate from distal genomic DNA sequences and are ligated adjacent to one another during circularization. Potential artifacts of this method include small inserts (lacking the linearizing restriction enzyme sequence), which are inward-facing [forward/reverse (FR)] (non-jumping) read pairs. In addition, chimeras result from the paired ends falling on different chromosomes, the insert size exceeding the maximum of 100 KB, or two times the mode of the insert size for outward-facing pairs. For additional information, see the Wikipedia article.