A podcast about computational biology, bioinformatics, and next generation sequencing.
https://bioinformatics.chat
Gesamtlänge aller Episoden: 3 days 1 hour 46 minutes
episode 10: Spatially variable genes and SpatialDE with Valentine Svensson
Valentine Svensson explains how he analyzes spatially-annotated single cell gene expression data using Gaussian processes...
episode 9: Michael Tessler and Christopher Mason on 16S amplicon vs shotgun sequencing
Michael Tessler and Christopher Mason join me to talk about their comparison of 16S amplicon sequencing and shotgun sequencing for quantifying microbial diversity.
Links:
- The 2017 Nature paper that we discuss: Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
-
Michael’s et al...
episode 8: Perfect k-mer hashing in Sailfish
The original version of Sailfish, an RNA-Seq quantification tool, used minimal perfect hash functions to replace k-mers with unique integers. (The current version appears to be using a Cuckoo hashmap instead.)
This is my attempt to explain how a minimal perfect hash function could be built. The algorithm described here is not exactly the same as the one Sailfish used, but it follows the same idea...
episode 7: Metagenomics and Kraken
What is metagenomics and how is it different from phylotyping?
What is Kraken and how can it be faster than BLAST?
Let’s try to sort this out...
episode 6: Allele-specific expression
I talk about allele-specific expression: why it arises and how it can be reliably detected...
episode 5: Relative data analysis and propr with Thom Quinn
In this episode, Thom Quinn and I explore different ways to transform and analyze relative data arising in genomics.
We also discuss propr, Thom’s R package to compute various proportionality measures...
episode 4: ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur
In this episode, I meet with Georg Stricker and Julien Gagneur from the Technical University of Munich to discuss ChIP-seq data analysis and their tool, GenoGAM...
episode 3: miRNA target site prediction and seedVicious with Antonio Marco
In this episode Antonio Marco talks about miRNA target site prediction and his tool, seedVicious.
Links:
- seedVicious preprint
- seedVicious manual
If you enjoyed this episode, please consider supporting the podcast on Patreon.
episode 2: Single-cell RNA sequencing with Aleksandra Kolodziejczyk
In this episode Aleksandra Kolodziejczyk talks about single-cell RNA sequencing.
Links:
- A review paper by Aleksandra
- Comparative analysis of single-cell RNA sequencing methods, including the cost table
- Power Analysis of Single Cell RNA‐Sequencing Experiments
- Monocle: a toolkit for analyzing single-cell gene expression experiments
- Questions from listeners on bioinformatics...
episode 1: Transcriptome assembly and Scallop with Mingfu Shao
In this episode, Mingfu Shao talks about Scallop, an accurate reference-based transcript assembler.
Links:
- The preprint about Scallop
- The preprint about flow decomposition
- The video of a talk by Ben Langmead about Rail-RNA
- The preprint about Rail-RNA
If you enjoyed this episode, please consider supporting the podcast on Patreon.