geuvadis_rna_analysis

geuvadis_rna_analysis@lists.crg.es

160 discussions

[Geuvadis_rna_analysis] important: action items for the main paper

by Tuuli Lappalainen

Hello, I've drafted the main paper and I'll send it to you for comments in 1-2 days. Before that, I want to fill in as many of the missing pieces as possible - I'm working hard on many of these, and some I need from you. We're not far from finish, but not quite there yet either. I've put together a list of action items, some of these I've already discussed with you individually. Please complete as many of these as you can *by Wednesday**6pm*, so that I can have them in the draft before I circulate it. The very serious deadline is on *Saturday* - I'll really need to have these by then if not by Wednesday. cheers, Tuuli - Jean: send sQTL data to Tuuli run Astalavista for GRB sQTLs, and send the numbers for Tuuli for final plotting send Supplementary Fig of transcript quantifications and a legend for it - Micha: finish the analysis of population frequency and annotated/novel junctions splice score distributions (REF & ALT for donor & acceptor): send the values to Tuuli for final plotting. - Gabrielle: figure out what will be the stable www address of the wiki - Matthias calculate how many splice junctions (out of total) have soft splicing in 1) any individual 2) all individuals. - Monkol send supplementary methods text of annotations send a table of variant counts in annotation classes - Natalja: send supplementary methods text of imputation protocol send supplementary methods text of visualization prepare an example plot of the quantification tracks - Peter/Maarten: prepare a prettier network figure (2d) and a legend for that prepare supplementary table of miRNA-mRNA associations send the formulae for supplementary methods - Peter/Irina: I'll get the repeat eQTLs to you on Wednesday morning (sorry for the delay, cluster problems) - after that, analyze them - Jonas: plot read count distributions for miRNA (and replot mRNA if it's easier to make the plots pretty and similar that way) plot gene count histograms for mRNA and miRNA - Manny: get numbers of LoF variants (total and covered by RNAseq data) estimate the number of stop+ that are truly NMD - Tuuli (FYI) analyze causal variant discovery and GWAS causal variants run independent eQTL analysis run sQTL-eQTL overlap run and plot annotation enrichments of sQTLs analyze rare variant mapping if there's time plot MDS for peer-corrected mRNA data polish text, legends and a few figure integrate comments, text and plots from others add references -- 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, 5 months

[Geuvadis_rna_analysis] analysis group TC Nov 15 at 2pm

by Tuuli Lappalainen

Hello all, We'll have an RNAseq analysis group TC today at 2pm CET. Apologies for the late notice. I hope many of you can attend since it's been a while due to me traveling; there are a number of important things to discuss: - updates from Santiago de Chile - updates from ASHG - outline, timeline and action items for the main paper - outlines, timelines and action items for the companion papers - analysis updates - 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 / 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, 5 months

[Geuvadis_rna_analysis] ASHG poster

by Tuuli Lappalainen

Hello all, Here's the almost-final draft of Geuvadis RNAseq poster for ASHG. I'll get it printed on Monday, so if you have any last minute comments or suggestions, please send them to me as soon as possible. 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, 6 months

[Geuvadis_rna_analysis] acknowledgement for funding - GEUVADIS RNAseq project

by Gabrielle Anne Bertier

Dear all, As decided during our Annual Meeting last week, we will include links to our data within EBI databases on the GEUVADIS web page. In this webpage we will include the full author list of the RNAseq paper and an embargo statement. At the request of Manolis and Tuuli, could you please send me the list of any additional funding source or agency that you want to acknowledge for this work apart from GEUVADIS ? Please do so ASAP, and before tomorrow Tuesday 10:00 CET, time when the page will go live. Thank you for your collaboration, and sorry for the last minute request, 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, 6 months

[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

12 years, 6 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

12 years, 6 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

12 years, 6 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

12 years, 6 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>

12 years, 6 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

12 years, 6 months

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