geuvadis_rna_analysis October 2012

geuvadis_rna_analysis@lists.crg.es

8 participants
19 discussions

[Geuvadis_rna_analysis] analysis group TC today 2pm

by Tuuli Lappalainen

Hello, We'll have a Geuvadis analysis group call today Oct 25th at 2pm CET. Apologies for the late reminder. On the agenda: - ASHG poster - analysis updates - sQTL presentation from Jean best, Tuuli 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 / -- 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

11 years, 11 months

[Geuvadis_rna_analysis] text and figures

by Tuuli Lappalainen

Hello all, I just wanted to thank all of you for material that you've sent me for the main paper - now you can have a relaxed weekend while I have a huge pile of stuff to read! I'll be going through all the material during the next week, and I'll be in touch with you if/when I need additional info. By the way, there's a free presentation slot on the next TC if someone wants to present. 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

11 years, 11 months

[Geuvadis_rna_analysis] eQTL files available

by Tuuli Lappalainen

Hi, I've uploaded the cis-eQTL files for exons and miRNAs in /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/qtl/eQTL/ . The wiki is outdated in terms of eQTL results, but the methods section should be correct. 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

11 years, 11 months

[Geuvadis_rna_analysis] sQTL and transcript variation slides for the TC

by Jean Monlong

Hi all, Here are the slides for the TC. I will present the results on splicing QTL and some analysis on transcript variation if we have time. Regards, Jean

11 years, 11 months

[Geuvadis_rna_analysis] Please forward - Petition to protect EU science budget

by Gabrielle Anne Bertier

Dear GEUVADIS partners, I would like to draw your attention to the petition from Anna Leptin. We highly encourage everybody to sign up and to forward it to colleagues at your institute and outside. http://www.no-cuts-on-research.eu Thanks Best 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 -----Original Message----- From: Maria Leptin [mailto:maria.leptin@embo.org] Sent: martes, 23 de octubre de 2012 02:13 p.m. Subject: Please forward - Petition to protect EU science budget Dear colleagues, The discussions at the next summit of the European Union heads of state or government, which is scheduled for 22 and 23 November, will be decisive in determining the EU research budget for the next seven years. Several Member States are demanding severe cuts on the total EU budget and research will have to compete with other policy priorities. This is a time when we, the scientific community, should act together and make our case to protect research funding, including that of the European Research Council (ERC), from cuts. Decisions will be prepared in discussions among politicians at the national level. All of us must look for opportunities to affect these decisions and send a strong signal to the heads of state or government. An open letter signed by European Nobel laureates has been published in top European newspapers this week. The impact of this letter will be increased if it is followed by a mobilization of the national scientific communities. To keep the momentum going, an online petition has been launched: http://www.no-cuts-on-research.eu I would like to ask you to sign it and to encourage all your colleagues to do likewise. Note that in the past, less than 30 000 scientists signed the largest petition for a European scientific cause compared to the hundreds of thousands of signatures on petitions from other groups of society. We must do better than that. This action is coordinated by the Initiative for Science in Europe (ise(a)i-se.org<mailto:ise@i-se.org>; www.initiative-science-europe.org<http://www.initiative-science-europe.org>), of which EMBO is a member. Please contact Wolfgang Eppenschwandtner, Executive Coordinator of the ISE if you have any questions or suggestions. Best regards, Maria Leptin Director EMBO - excellence in life sciences Meyerhofstr. 1 69117 Heidelberg, Germany tel +49-6221-8891-102 fax +49-6221-8891-202 maria.leptin(a)embo.org<mailto:maria.leptin@embo.org>

11 years, 12 months

[Geuvadis_rna_analysis] geuvadis paper guidelines

by Tuuli Lappalainen

Hello all, Here's some more info regarding the material that I've asked you to contribute to the Geuvadis main paper. The *deadline* for this was *today* but I'll extend it to next week's *Friday, October 26*. Thanks to those couple of people who actually made it on time. If you have some super-exciting additional analysis going on beyond that date, send me the rest and write a placeholder of what's missing. *Text*: As I said before, everyone who wants to have their analysis included in the main paper has to send me text that describes your methods, results and conclusions. We will likely end up having a supplementary text that is more than just methods, and I'll incorporate your text there, and we'll of course use this information when writing the main text. - Think of this as a mini manuscript, so please write proper text with full sentences. The text can and should be detailed, but don't overdo it; include only relevant and interesting analyses/results. - Refer to the figures/tables you provide with e.g. Fig. TUULI_1_samplecorrelation (your name, figure number, description) so that we can keep track of them. Write legends as well. - Include references to the literature as PubMed IDs *Figures*: The following has been written with plotting in R in mind - you can of course use other software, but try to follow these guidelines as much as possible. Nice figures are extremely important in making the paper attractive to editors, reviewers and readers. - 1-6 figures/tables per person is probably what we can include. - size: height=5, width=5 inches. Make *sure* that the plots look good when shrinked; they will be printed in max one column width which is much much less than a powerpoint slide or your screen. If you deviate from the square shape, keep in mind that most plots will be panels of a single figure and should fit together. - background must be white or transparent! - axis labels, legends and all other text included in the plot *must *be big enough. No exceptions. The default settings are hardly ever enough; in R, cex.axis=1.5, cex.lab=1.5, cex.names=1.5 is good for 5x5 inch images. - use the population and laboratory colors that have been defined in the sample information sheet - line width needs to be thick, 2 in most cases (lwd=2), e.g. in boxplots, most scatterplots. - save your figures as pdf vector graphic, in R the command is pdf() , with the file name like TUULI_1_samplecorrelation.pdf . - have your scripts organized so that you can reproduce figures easily if/when needed Please let me know if you have any questions. These instructions will hopefully save time and nerves from all of us, so that we can spend more time thinking and discussing about science rather than figure formats. cheers, Tuuli (also known as the Figure Nazi...) -- 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

11 years, 12 months

[Geuvadis_rna_analysis] Geuvadis TC October 19th at 4pm CET

by Tuuli Lappalainen

Dear all, We will have a Geuvadis RNAseq workpackage call on Friday October 19th at 4pm CET. Agenda: - Update on the analysis - Outlines of the papers: - main paper - QC companion - splicing companion - loss-of-function companion - Publication and authorship - 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 /People calling from CRG: Recently there have been some problems in calling to the Spanish number above. The problem seems to be in your end, and Gabrielle is checking what can be done. If it doesn't work, please call e.g. to the German number. 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] analysis group TC October 18

by Tuuli Lappalainen

Hello, We'll have a Geuvadis analysis group call on Thursday October 18th at 2pm CET. On the agenda: - analysis updates; in particular asQTLs and miRNA-mRNA interactions - RNA editing presentation by Thomas - if there's time, allele-specific alternative splicing slides by Tuuli best, Tuuli 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 / -- 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] analysis group call October 11 at 2pm

by Tuuli Lappalainen

Hello, We'll have an analysis group call on Thursday October 11 at 2pm CET. On the agenda: - analysis updates - figures for the main paper - deadlines for the paper(s) - splicing presentation by Micha - allele-specific splicing presentation by Tuuli if there's time 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, 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] RNA editing results

by Thomas Wieland

Hi, here some updates on the analysis we've done on RNA editing: http://sanabre.net/geuvadis/index.php/A2_Variant_Calling#Variant_calling_at… Best Regards, Thomas -- Thomas Wieland Tel: +49 89 3187 2169 PhD Student Bioinformatics Fax: +49 89 3187 3297 Institute of Human Genetics http://ihg.helmholtz-muenchen.de Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Ingolstädter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht München HRB 6466 USt-IdNr: DE 129521671

12 years

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geuvadis_rna_analysis October 2012