SeqMonk tools for methylation analysis

Slides:

Advertisements

Similar presentations

Beatriz Martinez - SAT CFA Team 2 nd CFA Implementation Review ESAC, Madrid, 06 Jun 2013 CLUSTER FINAL ARCHIVE (CFA) Future developments.

Advertisements

EiS – Education iT Services “Our passion in EiS is to make a real difference in education and ultimately children’s lives by providing innovative solutions.

Differential Methylation Analysis

Visualising and Exploring BS-Seq Data

The Maize Inflorescence Project Website Tutorial Nov 7, 2014.

Simon v2.3 RNA-Seq Analysis Simon v2.3.

1000 Genomes SV detection Boston College Chip Stewart 24 November 2008.

1 TiVi70 – Skin Colour Tracker Welcome to the presentation of.

Quantitative Trading Strategy based on Time Series Technical Analysis Group Member: Zhao Xia Jun Lorraine Wang Lu Xiao Zhang Le Yu.

Supplementary Material Supplementary Tables Supplementary Table 1. Sequencing statistics for ChIP-seq samples. Supplementary Table 2. Pearson correlation.

Graphing A Practical Art. Graphing Examples Categorical Variables.

Proliferation cluster (G12) Figure S1 A The proliferation cluster is a stable one. A dendrogram depicting results of cluster analysis of all varying genes.

Galaxy for Bioinformatics Analysis An Introduction TCD Bioinformatics Support Team Fiona Roche, PhD Date: 31/08/15.

RNA-Seq Analysis Simon V4.1.

EDACC Primary Analysis Pipelines Cristian Coarfa Bioinformatics Research Laboratory Molecular and Human Genetics.

I519 Introduction to Bioinformatics, Fall, 2012

Presenting Results Laura Biggins v1.0 1.

EDACC Quality Characterization for Various Epigenetic Assays

1 Original Source : and Problem and Problem Solving.ppt.

Chapters 2 & 3 MATLAB Skills This tutorial revisits Examples 3.1 to 3.4 to show how MATLAB can be used to solve the same problems 1.Scatter Plots 2.Other.

Tutorial 6 High Throughput Sequencing. HTS tools and analysis Review of resequencing pipeline Visualization - IGV Analysis platform – Galaxy Tuning up.

Test status report Test status report is important to track the important project issues, accomplishments of the projects, pending work and milestone analysis(

Quality Control and Target Validation in Sequencing v1.0 Simon Andrews Laura Biggins Boo Virk.

-1- Module 3: RNA-Seq Module 3 BAMView Introduction Recently, the use of new sequencing technologies (pyrosequencing, Illumina-Solexa) have produced large.

A Routine Approach to Quality Control Peter Haberl

SUPPORTING INFORMATION Figure S1. Cotton whitefly infestation within a sealed chamber.

Biocomputational Languages December 1, 2011 Greg Antell & Khoa Nguyen.

HOMER – a one stop shop for ChIP-Seq analysis

TRACKSTER &CIRCSTER DEMO Slides: /g/funcgen/trainings/visualization/Demos/Trackster+Circster.ppt Galaxy: Galaxy Dev:

Using Galaxy to build and run data processing pipelines Jelle Scholtalbers / Charles Girardot GBCS Genome Biology Computational Support.

Data Coaching Services Chart Interpretation 1. o Bar o Stacked Bar o Pie o Line o Scatter plot 2.

Visualizing data from Galaxy

Misleading bioinformatics: Mistakes, Biases, Mis-interpretations and how to avoid them Festival of Genomics 2017 Course Exercise Material:

Differential Methylation Analysis

Simon v RNA-Seq Analysis Simon v

SeqMonk tools for methylation analysis

Data analysis tools - quantitative

SeqMonk tools for methylation analysis

Simon v1.0 Motif Searching Simon v1.0.

Supplementary Figure 1 A B C.

DNA Methylation Regulates Gene Expression in Intracranial Aneurysms

Noise issues – Potentiometer signal from the electronic card

Understanding and Validating Experimental Expectations

From: Optimized design and assessment of whole genome tiling arrays

Analysing ChIP-Seq Data

Figure 1. Complete work-flow of the Scasat

Simon v ChIP-Seq Analysis Simon v

ChIP-Seq Data Processing and QC

Exploring and Understanding ChIP-Seq data

by David M. Weinstock, Beth Elliott, and Maria Jasin

Misleading Bioinformatics Mistakes, Biases, Mis-Interpretations and how to avoid them Festival of Genomics 2017.

Visualising and Exploring BS-Seq Data

Sequence features that were correlated with ASD.

Eric Samorodnitsky, Jharna Datta, Benjamin M

Genome-wide DNA methylation profile implicates potential cartilage regeneration at the late stage of knee osteoarthritis Y. Zhang, N. Fukui, M. Yahata,

The Translational Landscape of the Mammalian Cell Cycle

The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin

Volume 21, Issue 5, Pages e7 (November 2017)

Epigenetic regulation of miR-193b in liposarcomagenesis.

Volume 133, Issue 3, Pages (May 2008)

Simon V Motif Searching Simon V

Genome-wide sperm deoxyribonucleic acid methylation is altered in some men with abnormal chromatin packaging or poor in vitro fertilization embryogenesis

Expression Quantitative Trait Loci Analysis Identifies Associations Between Genotype and Gene Expression in Human Intestine Boyko Kabakchiev, Mark S.

Exploring and Presenting Results

Supplementary Figure 1 A B C.

Comparison of proteomics and RNA‐Seq data.

Density Density ß values ß values

Elevated DNA methylation across a 48-kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology Rebecca G. Smith,

Presentation transcript:

SeqMonk tools for methylation analysis Simon Andrews simon.andrews@babraham.ac.uk @simon_andrews

SeqMonk

SeqMonk Data Model Conventional data (ChIP-Seq, RNA-Seq etc) Data is reads (BAM files etc) Strand indicates genomic strand BS-Seq and related data Data is methylation calls All ‘reads’ are 1bp in length Strand indicates meth state (+=meth -=unmeth) Original strand comes from the imported file

Raw Data Red = Meth Blue = Unmeth

Raw Data Display View > Data Track Display

Targeting Measurement Features Data > Define Probes > Feature Probe Generator

Targeting Measurement Fixed Windows Data > Define Probes > Running Window Generator

Targeting Measurement Fixed number of calls Data > Define Probes > Even Coverage Probe Generator

Targeting Measurement Fixed number of call positions Data > Define Probes > Read Position Probe Generator

Methylation Measurement Simple percentage of all calls Data > Quantitate Existing Probes > Difference Quantitation

Methylation Measurement More complex corrected measure Data > Quantitation Pipelines > Bisulphite methylation over features

Visualisation of quantitated methylation View > Data Track Display View > Set Data Zoom Level

Distributions Plots > Probe value histogram Plots > Cumulative Distribution Plot

Comparisons Plots > Scatter plot

Trend Plots Plots > Quantitation Trend Plot

Clustering Plots > Hierarchical Clusters Correlation based Euclidean Plots > Hierarchical Clusters