geuvadis_rna_analysis August 2012

geuvadis_rna_analysis@lists.crg.es

5 participants
16 discussions

[Geuvadis_rna_analysis] analysis group TC Aug 30th

by Tuuli Lappalainen

Hello all, We'll have a Geuvadis analysis group call on Thursday the 30th at 2pm CET. On the agenda: - I'll present slides of eQTL mapping in Geuvadis, mostly from methods point of view but with some early results. - The third analysis group meeting - due to my upcoming but still unscheduled knee surgery I unfortunately can't commit to hosting a meeting in October even in Geneva let alone elsewhere, so I suggest that we call this off for now. We can discuss more on the call. - Other analysis updates - AOB Call details are: from outside spain; 0034917911859 <tel:0034917911859> from spain; 900800678 Access code; 3160100 best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 1 month

[Geuvadis_rna_analysis] GEUVADIS Meeting and survey to distribute !

by Gabrielle Anne Bertier

Dear all, I remind you that there are just 4 days left before the deadline to register for our next Annual Meeting (preliminary program attached) PS: registration form full link: https://docs.google.com/spreadsheet/viewform?formkey=dEpnY0h6Y2Z3Y291dFhvRz…<https://docs.google.com/spreadsheet/viewform?formkey=dEpnY0h6Y2Z3Y291dFhvRz…> In preparation of the Workshop, and to collect quantitative and qualitative information on the status of NGS in Europe, we have constructed a survey<https://qtrial.qualtrics.com/SE/?SID=SV_bHJDue550PwdFrv> to be distributed to all Research and/or clinical institutions using NGS in Europe. The survey covers the following aspects: Technology available (number/type of sequencers, nb of runs, capture method) - Data Use (clinical/research uses) - Patients/participants (origin of samples, consent forms, incidental findings...) - Data storage - Data analysis (general information on analysis pipelines) - Clinical data management - Problems and suggestions. We would highly appreciate if you could distribute this survey to all your relevant colleagues working in such centers, and fill in the survey for your own institution. We'll also send this survey to the European and National Societies of Human Genetics, and the more responses we get the better ! Deadline to respond to the survey: 30th September 2012 Full survey link: https://qtrial.qualtrics.com/SE/?SID=SV_bHJDue550PwdFrv To describe the survey please use freely the following text: ------------------ THE GEUVADIS PROJECT - More information on our website: www.geuvadis.eu<file:///C:\Users\gbertier\Documents\GEUVADIS\Annual%20Meeting%202\www.geuvadis.eu> The latest high-throughput next-generation sequencing technologies allow investigators to sequence entire human genomes and transcriptomes at an affordable price and within a short time frame. An increasing number of research centers in Europe have access to these technologies, in-house or through regional, national and international infrastructures. Storing, disseminating and analysing the large amount of data produced generate major challenges. Tackling these challenges requires extensive exchange of data, information and knowledge between sequencing centers, bio-informatics networks, the medical research community and the industry at the European level. The GEUVADIS (Genetic EUropean VAriation in DISease) Consortium has four main aims: 1. Develop standards in quality control and assessment of sequence data 2. Develop models for sequencing data storage, access and exchange 3. Develop standards for the handling, analysis and interpretation of sequencing data from DNA (and RNA) 4. Develop guidelines on the handling of ethical, legal and social implications of phenotype prediction from sequence variation * PURPOSE OF SURVEY 1. Collect quantitative and qualitative information on the current status of DNA sequence production, storage, exchange and analysis in Europe. 2. Collect feedback from research/clinical centers on their main challenges and difficulties regarding the management of these large data-sets potentially containing important medical information 3. Collect information on local standardization efforts, and avoid duplication of efforts throughout Europe 4. Create a road-map/policy document outlining the necessary steps to take national standards to the European level * POTENTIAL PUBLICATION OF RESULTS 1. Results of this survey will be presented at an internal GEUVADIS workshop, on October 30-31st 2012. 2. We will disseminate the road-map to potential funders (private of public), including the European Commission and other possible national public funders. 3. We will submit an abstract to the Joint Conference of Human Genome Meeting 2013 and 21st International Congress of Genetics. * DEADLINE: 30.09.2012 --------------------- If you have any question or comment regarding the Annual Meeting, the workshop and/or the survey please don't hesitate to contact me. Kind regards, Gabrielle.- Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Tel: +34933160374 Mobile: +34639960656 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu; www.fliact.eu

12 years, 1 month

[Geuvadis_rna_analysis] pdfs in the wiki

by Tuuli Lappalainen

Hello, To embed pdf files in the wiki: {{pdf_embed | file-name.pdf | PDF document title}} best, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 1 month

[Geuvadis_rna_analysis] ASE results available

by Tuuli Lappalainen

Hello, At last I've finished running the allele-specific expression analysis for all the Geuvadis samples. The master file is available in : /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/ase See the wiki (http://sanabre.net/geuvadis/index.php/Allele_specific_expression) for details of the analysis. Variant annotation info is included in the files; more details again in the wiki (http://sanabre.net/geuvadis/index.php/Variant_annotation). I will be working on the analysis of these data in the next couple of weeks - I'll produce the basic stats and descriptions of ASE, look at the population genetics of ASE, and see how far we can get with mapping of rare regulatory variants. I've also recently developed a pipeline for analyzing allele-specific splicing (ASS :-) ) in a genome-wide manner, but more about that later... have a nice weekend, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 1 month

[Geuvadis_rna_analysis] eQTL methods in the wiki

by Tuuli Lappalainen

Hello all, I've written a pretty detailed description of the Geuvadis eQTL mapping methods in the wiki: http://sanabre.net/geuvadis/index.php/Basic_methodology By the way, when you're editing text, below the edit window there is a link to Editing help. I've written some instructions there, and please feel free to add more content if you've figured out a way to do some wiki editing that wasn't entirely trivial. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 1 month

[Geuvadis_rna_analysis] basic miRNA analyses uploaded

by Marc Friedlaender

Hello, as Tuuli mentioned, I have uploaded the results of the basic miRNA analyses to the ebi server at: ftp://ftp-private.ebi.ac.uk/upload/geuvadis/wp4_rnaseq/main_project/analysis_data/mirna/ There is a README file which supplies description of files and methods. I will lift the README to the wiki tomorrow. The analyses include phred scores, clipped reads, mappings, annotation breakdowns and summary statistics. cheers, Marc Marc Friedländer, Ph.D. Xavier Estivill laboratory Genes and Disease programme Centre for Genomic Regulation (CRG) C/ Dr. Aiguader, 88 08003 Barcelona, Spain Phone: +34 933160203

12 years, 1 month

[Geuvadis_rna_analysis] Analysis group TC August 23rd

by Tuuli Lappalainen

Hello, We'll have a Geuvadis RNAseq analysis group TC on Thursday August 23rd at 2pm. On the agenda: - the next analysis group meeting - presentation by Matthias about soft splicing (probably, if the phone system of their new building allows him to call in) - other analysis updates - AOB Call details are: from outside spain; 0034917911859 <tel:0034917911859> from spain; 900800678 Access code; 3160100 best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 1 month

[Geuvadis_rna_analysis] No analysis group TC on the 15th

by Tuuli Lappalainen

Dear all, Let's cancel the Geuvadis analysis group TC that we had planned for tomorrow, August 16th, due to vacation time and other obstacles. The next call will be on Thursday August 23th. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 2 months

[Geuvadis_rna_analysis] analysis group face-to-face meeting

by Tuuli Lappalainen

Hello, We need to decide if we want to organize a third Geuvadis RNAseq analysis group face-to-face meeting, and if yes, where and when this would be. I put together a small poll - please reply by Friday 24th of August: https://docs.google.com/spreadsheet/viewform?formkey=dGhhRkVCSllrNEdTYVlSZ3… best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 2 months

[Geuvadis_rna_analysis] Analysis group TC on Aug 9th

by Tuuli Lappalainen

Hello all, We'll have a Geuvadis analysis group call on Thursday August 9th at 2pm as usual. Apologies for the late notice. On the agenda: - The new wiki - The (possible) third analysis group meeting next fall - I'll present some slides about QC and technical covariates - AOB We'll continue discussing the QC companion paper with Peter et al. after the main call. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 2 months

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

geuvadis_rna_analysis August 2012