The bioinformatics chat is a podcast about computational biology, bioinformatics, and next generation sequencing.
The bioinformatics chat is produced by Roman Cheplyaka.
June 29, 2018
In this episode I’m joined by Chang Xu. Chang is a senior biostatistician at QIAGEN and an author of smCounter2, a low-frequency somatic variant caller. To distinguish rare somatic mutations from sequencing errors, smCounter2 relies on unique molecular identifiers, or UMIs, which help identify multiple reads resulting from the same physical DNA fragment.
Chang explains what UMIs are, why they are useful, and how smCounter2 and other tools in this space use UMIs to detect low-frequency variants.
May 31, 2018
Linear mixed models are used to analyze GWAS data and detect QTLs. Andrey Ziyatdinov recently released an R package, lme4qtl, that can be used to formulate and fit these models. In this episode Andrey and I discuss linear mixed models, genome-wide association studies, and strengths and weaknesses of lme4qtl.
April 30, 2018
In this episode Kristian Davidsen and Amrit Dhar present their project called SPURF. SPURF can predict the B cell receptor (BCR) substitution profile of a given clonal family based on a single representative sequence from that family. SPURF works by fitting a tensor regression model to publicly available Rep-seq data.