geuvadis_rna_analysis

geuvadis_rna_analysis@lists.crg.es

160 discussions

[Geuvadis_rna_analysis] presentation for today's TC

by P.A.C._t_Hoen＠lumc.nl

Dear all Please find attached a document describing an approach and initial results for miRNA:mRNA integration that Maarten van Iterson will discuss during today's TC Peter Dr. Peter A.C. 't Hoen Center for Human and Clinical Genetics Leiden University Medical Center Postal zone S4-P PO Box 9600 2300 RC Leiden The Netherlands phone: +31-71-5269421 fax: +31-71-5268285 e-mail: p.a.c.hoen(a)lumc.nl

12 years

[Geuvadis_rna_analysis] Geuvadis RNA analysis TC today - Details

by Gabrielle Anne Bertier

Dear all, This is a reminder of our TC today at 14:00 CET Here are the details of the call: Agenda Analysis updates Presentation from Leiden After the main call we'll continue with a subgroup to discuss splicing analyses; anyone interested is welcome to stay for that too. Dial-in Germany 08001013982 Netherlands 0107994092 Spain 900800678 Sweden 0752400458 Switzerland 0800705347 United Kingdom 08005285280 United States 3032489677 Access code: 3160100

12 years

[Geuvadis_rna_analysis] GEUVADIS RNAseq paper -- TC doodle

by Gabrielle Anne Bertier

Dear all, Please fill in the following doodle for the next GEUVADIS RNAseq TC on the project's publication: http://www.doodle.com/pdeyynfz3rnwvtaf?lt=2<http://www.doodle.com/pdeyynfz3rnwvtaf?lt=1> Preliminary agenda would be: - outlines of the main paper and the QC companion paper - practicalities of publication - other companion papers 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

[Geuvadis_rna_analysis] QC and data updates

by Tuuli Lappalainen

Hello, A couple of data and analysis updates: - QC: I've reran the plots of sample correlations and clustering using the correlation matrices provided by Peter. The total dataset shows clustering by lab rather than populations (probably because systematical differences between these populations are not that big), but the replicate samples look very good with lab effects being less than biological variation. See http://sanabre.net/geuvadis/index.php/MRNA#Sample_correlation_and_clusterin… - Splice junctions for Manny: I've normalized the junctions by total gene count, to able able to extract splice changes from variation in overall expression level. The files of these with subsequent transformation to standard normal are in /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/quantification/splice_junction-intron , file names with GeneN. 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

[Geuvadis_rna_analysis] IMPORTANT NOTICE: GEUVADIS survey DEADLINE EXTENDED

by Gabrielle Anne Bertier

Dear all, I remind you that we would highly appreciate if you could fill in, and distribute our survey on NGS to all your relevant colleagues. Note that we've extended the deadline to the 10th October 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

[Geuvadis_rna_analysis] Analysis group TC September 27th

by Tuuli Lappalainen

Hello, We'll have our regular Geuvadis RNAseq analysis group call on September 27th at 2pm CET. Agenda: - agenda for the whole group call within 2 weeks - presentations in Santiago de Compostela - draft of the main paper outline by Tuuli - we need to come up with a good common statistics (or two) to describe population variation of different transcriptome features - Manny will presentation on loff-of-function splice variant effects Call details: Germany +49 692 573 804 41 <tel:%2B49%20692%20573%20804%2041> Netherlands +31 108 920 271 <tel:%2B31%20108%20920%20271> Spain +34 931 816 661 <tel:%2B34%20931%20816%20661> Sweden +46 840 309 949 <tel:%2B46%20840%20309%20949> Switzerland +41 58 262 07 22 <tel:%2B41%2058%20262%2007%2022> United Kingdom +44 203 370 57 19 <tel:%2B44%20203%20370%2057%2019> United States +1 646 381 08 89 <tel:%2B1%20646%20381%2008%2089> /Access code: 611683 / 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

[Geuvadis_rna_analysis] "problem" editing one of the wiki pages

by Jean Monlong

Sorry for the bad connection of my phone/skype(at least I can here you very well), Anyway the page I was talking about is http://sanabre.net/geuvadis/index.php/%28A3%29_mRNA_Variation I can edit the other one but this one no. Thanks, Jean

12 years

[Geuvadis_rna_analysis] IMPORTANT REMINDER: GEUVADIS survey to fill in and distribute !

by Gabrielle Anne Bertier

Dear all, I remind you that we would highly appreciate if you could fill in, and distribute our survey on NGS to all your relevant colleagues. I have attached a PDF describing all questions you will face in the survey 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

[Geuvadis_rna_analysis] analysis group TC on September 20

by Tuuli Lappalainen

Hello, Let's have our weekly Geuvadis analysis group TC on Thursday September 20 at 2pm CET. On the agenda: - Analysis updates (that we didn't have time to do last week) - Matthias's slides on splicing - AOB Call details: Germany +49 692 573 804 41 <tel:%2B49%20692%20573%20804%2041> Netherlands +31 108 920 271 <tel:%2B31%20108%20920%20271> Spain +34 931 816 661 <tel:%2B34%20931%20816%20661> Sweden +46 840 309 949 <tel:%2B46%20840%20309%20949> Switzerland +41 58 262 07 22 <tel:%2B41%2058%20262%2007%2022> United Kingdom +44 203 370 57 19 <tel:%2B44%20203%20370%2057%2019> United States +1 646 381 08 89 <tel:%2B1%20646%20381%2008%2089> /Access code: 611683 / cheers, 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

[Geuvadis_rna_analysis] normalized miRNA quantifications

by Tuuli Lappalainen

Hello all, I've uploaded normalized miRNA quantifications to the ftp site: /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/mirna/quantification_tables . See wiki (http://sanabre.net/geuvadis/index.php/Basic_methodology) for details. There are files for: - 363 European QC-passed samples, corrected with 10 PEER factors (including population and seqlab). - 89 Yoruba QC-passed samples, corrected with 5 PEER factors (including seqlab). These files should be considered slightly preliminary - it is possible that we'll end up using these in the end, but before freezing this I want to do some covariate analysis (once I get the fastq QC stats). We should do eQTL analysis separately for EUR and YRI, but as we discussed on the call, miRNA-mRNA correlations could maybe be done on the whole dataset after correcting for population. I'll produce these files in ~1 week - for this I'll also need to normalize the mRNA data in a similar manner, and that takes more time to run. In the meanwhile you can probably use the population-specific data. cheers, 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

← Newer
1
2
3
4
5
6
7
8
...
16
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

geuvadis_rna_analysis