the bioinformatics chat

By Roman Cheplyaka

A podcast about computational biology, bioinformatics, and next generation sequencing.... more

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FAQs about the bioinformatics chat:

How many episodes does the bioinformatics chat have?

The podcast currently has 70 episodes available.

the bioinformatics chat episodes:

September 03, 2017#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.

Links:
Valentine’s preprint, “SpatialDE - Identification Of Spatially Variable Genes”

SpatialDE code on GitHub

Valentine’s personal page

The Integrative Biology & Medicine conference

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58min
August 18, 2017#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. 2016 paper that describes their original 16S study: A Global eDNA Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil

The sequencing data for these studies is available from NCBI:
PRJNA310230
(16S),
PRJNA389803
(shotgun)

Michael’s website

Christopher’s lab website

The Integrative Biology & Medicine
conference, featuring the talk on Postmodern Synthesis by Eugene Koonin

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46min
August 05, 2017#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.

Sections:
Sailfish and perfect hashing (1:15)

Perfect hashing based on binary search or hash tables (4:34)

Random hash functions (7:34)

Perfect hash function based on an acyclic graph (12:16)
Links:
The Sailfish paper

The paper describing the perfect hashing algorithm

The birthday paradox

Integrative Biology & Medicine

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23min
July 09, 2017#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.

Sections:
Culturing and its limitation (00:18)

Metagenomics vs phylotyping (1:43)

BLAST (5:53)

The idea behind Kraken (8:14)

How Kraken organizes its database (18:08)
Links:
The paper about Kraken

A freely accessible (though a bit dated) book on metagenomics
Correction: in this episode, I incorrectly state that Kraken operates on
phylogenetic trees, whereas in fact it operates on taxonomic trees.
In practice this means that when Kraken cannot decide among several species,
it assigns the read to their lowest common taxon (genus, family etc.),
not their latest common evolutionary ancestor.

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29min
June 25, 2017#6 Allele-specific expression
I talk about allele-specific expression: why it arises and how it can be
reliably detected.

Sections:
The biology of allele-specific expression (2:17)

Detecting allele-specific expression with RNA-seq (7:46)

Mapping and sequencing biases (16:39)

The experiment in yeast (19:47)

Statistical models (21:44)
Links:
A powerful and flexible statistical framework for testing hypotheses of
allele-specific gene expression from RNA-seq data
Supplemenal information

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

The talk by John Marioni

The blog post explaining the RSEM model

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34min
June 10, 2017#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.

Links:
Thom’s preprint about propr —
take a look if you feel lost in all the quantities that we discuss :)

David Lovell original paper introducing proportionality for relative data
and a very detailed appendix

Ionas Erb’s paper introducing the ρ metric

Vignettes for propr

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56min
May 29, 2017#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.

Links:
Preprint about GenoGAM

Georg on GitHub

Julien’s lab on Twitter

[BC]2 — The Basel Computational Biology Conference (Basel, September 2017), where you can meet Georg

The European Human Genetics Conference (Copenhagen, May 2017), where you can meet Daniel Bader from Julien’s lab
Register for the Summer School in Bioinformatics & NGS Data Analysis (#NGSchool2017) (Poland, September 2017)

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56min
May 12, 2017#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

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57min
April 29, 2017#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.chat
and
reddit

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1h 9min
April 16, 2017#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

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44min

FAQs about the bioinformatics chat:

How many episodes does the bioinformatics chat have?

The podcast currently has 70 episodes available.

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