Renaud Massart

Questions and Answers (3) View all

• Answer added in Epigenetics
  6 Software for next generation sequencing data, microarray data.
  By Renaud Massart · McGill University
  Renaud Massart · McGill University

  Thank you for your replies. In our lab., we're starting having a really large amount of data from MeDIP-arrays, mRNA microarrays, RNAseq and DNAseq ex... [more]

  Thank you for your replies. In our lab., we're starting having a really large amount of data from MeDIP-arrays, mRNA microarrays, RNAseq and DNAseq experiments (bisulfite -or not- converted DNA). Most of the people of the lab are not bioinformaticians and as the bioinformatician is overloaded, we're facing problems when it comes to analyze the data (basic statistical analyzes for ex.) but also when it comes to manage the big files generated by the analyzes. Thus, we're learning how to use R environment... However, I would like to know if good friendly softwares (or suites) could be recommended to analyze or integrate data from various "whole-genome" experiments.
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• Question asked in Epigenetics
  6 Software for next generation sequencing data, microarray data.
  Could anyone recommend "friendly" softwares or software suites (genomatix... ?) to analyze and integrate whole genome sequencing and/or microarrays da... [more]
  Could anyone recommend "friendly" softwares or software suites (genomatix... ?) to analyze and integrate whole genome sequencing and/or microarrays data?
  By Renaud Massart · McGill University
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• Answer added in DNA Sequencing
  16 Epigenetics and DNA sequencing?
  By Ralph Scheicher · Uppsala University
  Renaud Massart · McGill University

  Be careful with pyrosequencing (or bisulfite sequencing) methylated and non-methylated DNA sequences are amplified differently (after or not bisulfite... [more]

  Be careful with pyrosequencing (or bisulfite sequencing) methylated and non-methylated DNA sequences are amplified differently (after or not bisulfite conversion). This could induces biases during PCR amplifications and the biases are sequences specific. Therefore, controls are necessary to be sure of the levels of methylation that are measured. For instance, you need to generate a mixture of the DNA sequence that you want to analyze with a methylation level of 50% and be sure that you are able to measure a methylation level of 50%... This is not straight forward... Furthermore, pyrosequencing is not really convenient to detect non CG methylation. This kind of biases are not really known when using next generation sequencing technics...
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