Brendel Group Presentation: 5 Nov 2013
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Slides from my debriefing of the Cold Spring Harbor Lab Genome Informatics meeting I attended 30 Oct-2 Nov 2013.
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In this webinar, Dr. Raed Samara will cover:
1. Fusion genes: what they are and a historical perspective
2. Fusion gene detection: the current status
3. RNA sequencing vs. digital RNA sequencing
4. How to detect and accurately quantify novel fusion genes in your sample
Virus analysis
The document discusses research issues in virus analysis. It summarizes the antivirus detection process, malware analysis process, and research issues in antivirus labs and on desktops. Some key challenges mentioned are sample collection and filtering, signature distribution at scale, prevention, detection, and recovery techniques on desktops. The document also provides an overview of the current state of antivirus technologies like heuristics, signature updates, and efforts toward automation in antivirus labs.
DNA Sequence Data in Big Data Perspective
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Tools for Using NIST Reference Materials
This document discusses the Genome in a Bottle Consortium's efforts to develop reference materials and standards to validate next generation sequencing assays. It provides an overview of the consortium's goals to generate reference genomes with highly confident variant calls and accompanying data to allow labs to compare results and assess false positives and false negatives. The document describes some examples of how labs are using the consortium's data on the NA12878 genome to benchmark sequencing platforms and bioinformatics workflows.
Use of NCBI Databases in qPCR Assay Design
The document discusses using NCBI databases to design quantitative PCR (qPCR) assays. It describes several NCBI tools that can be used:
1) The NCBI Nucleotide and Gene databases to obtain sequence information for the gene of interest.
2) NCBI BLAST to perform sequence searches and check primer specificity against relevant databases.
3) NCBI dbSNP to search for single nucleotide polymorphisms (SNPs) in the primer binding sites that could affect assay performance.
The document provides guidance on how to use these NCBI tools at various steps of the qPCR assay design process.
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Brendel Group Presentation: 6 Mar 2013
The document compares different assembly algorithms for constructing transcripts from RNA-seq data: Butterfly, PASA, and CuffLinks. It analyzes eight assemblies that vary the algorithm and use of digital normalization. Butterfly produced the most transcripts while PASA and CuffLinks were more conservative. PASA and CuffLinks assemblies were more robust to digital normalization. The document proposes additional statistical analyses and using an expectation-maximization algorithm to discern isoforms.
Brendel Group Presentation: 4 Mar 2013
The document discusses three algorithms for reconstructing transcripts from RNA-Seq data that are available in the Trinity RNA-Seq package: Butterfly, PASA, and Cufflinks. Butterfly aims to enumerate all plausible transcripts supported by reads, PASA finds the largest assembly containing each alignment, and Cufflinks identifies the minimal set of transcripts needed to explain the read mappings. The presentation will next compare results from running Trinity with these three algorithms on two different RNA-Seq datasets.
Brendel Group Presentation: 21 Nov 2013
The document summarizes Daniel Standage's analysis of differential gene expression in the paper wasp Polistes dominula. He performed locus-level differential expression analysis after isoform-level analysis proved unreliable. The genome contains 18,675 intervals (iLoci) partitioned by gene content. Initial analysis found 295 differentially expressed iLoci but sample grouping was problematic. After filtering iLoci by read counts and re-running the analysis without a problematic sample, 314 differentially expressed iLoci were identified, mostly over-expressed in workers. Cytochrome P450 and NADH dehydrogenase genes were frequently differentially expressed.
Brendel Group Presentation: 19 Nov 2013
The document discusses cytochrome P450 (CYP) genes that were found in the genome of the paper wasp Polistes dominula. CYP genes encode oxidation enzymes and play important roles in insects, including metabolizing exogenous compounds and regulating endogenous compounds like juvenile hormone and ecdysone. The analysis of P. dominula found many differentially expressed CYP genes. CYP genes have been associated with caste determination in other social insects through their links to juvenile hormone.
Brendel Group Presentation: 15 Oct 2013
This document discusses RSEM, a tool for accurate transcript quantification from RNA-seq data. RSEM uses expectation maximization to estimate transcript expression levels without requiring a reference genome. It handles multireads better than other tools by either discarding, rescuing, or estimating maximum likelihood expression levels. Evaluation on simulated data showed RSEM had higher accuracy than other tools like Cufflinks and rQuant.
Brendel Group Presentation: 17 Oct 2013
The document describes a study that analyzed differential gene expression between queen and worker castes of the paper wasp Polistes dominula. 12 samples (6 queens and 6 workers) were collected from different colonies. Initial analysis found thousands of differentially expressed transcripts but permutation testing showed this was likely due to noise. Additional filtering reduced the number of transcripts and samples analyzed. The top differentially expressed transcripts were presented, with one transcript showing a fold change of 126 between castes.
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Brendel Group Presentation: 5 Nov 2013
- 1. CSHL Genome Informatics: debriefing Daniel S. Standage, 5 Nov 2013
- 2. Themes RNA-Seq Genomic variation Technical details matter Reproducibility Web-based tools
- 3. RNA-Seq De novo assembly Sreeram Kannan, Lior Pachter, David Tse Bayesembler Quantification Sailfish Lior Pachter?
- 4. Genomic variation MedSavant GEMINI SCALPEL: indel ID via NGS Others Genome rearrangements SNPs
- 5. Technical details matter Reproducibility Software engineering Cyberinfrastructure Clear description of methods
- 6. Software engineering protips Version everything Test everything (and automate those tests) Review everything Measure everything Engage users
- 7. Reproducibility Don’t rely on a single assembly Don’t rely on a single source of annotation Genome sequenced twice at deep (60x) coverage, variants ID’d; only 94% agreed
- 8. Web-based tools Utilize ubiquitous browser Most are open source, some offer VM distro APIs and SDKs integration extension programmatic access
- 9. A few talks of interest Mario Stanke: comparative gene finding Lior Pachter: RNA-Seq methods, units Michael Snyder: integrative “Snyderome” Sreeram Kannan: RNA-Seq assembly Rob Patro: Sailfish Chung-chao Hon: natural antisense transcripts