geuvadis_rna_analysis November 2012

geuvadis_rna_analysis@lists.crg.es

4 participants
7 discussions

[Geuvadis_rna_analysis] Analysis group TC November 29th

by Tuuli Lappalainen

Hello, We'll have a Geuvadis RNAseq analysis group TC on November 29th at 2pm CET. It will probably be a relatively short call. The agenda: - contents of the papers (main & companions) - timelines of the papers - LoF collaboration with the GTEx consortium - 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, 4 months

[Geuvadis_rna_analysis] main paper draft

by Tuuli Lappalainen

Hello all, Here is the draft of the Geuvadis main paper for the analysis group to read and comment. It's still a bit rough, but you get the idea. I'd like to ask you to send comments to me by *Saturday noon* - track changes in word, or write comments in an email. There are still some analysis items and material missing; see the updated action items below and please *complete your tasks**as soon as possible, by Saturday noon at the very latest. * The schedule is tight because we can't let our competitors get too far ahead of us. I'll aim to finish at least 99% of the numbers, results, and changes suggested by you by early next week, after which we circulate the paper with the whole group and submit in early December. There are 5 files: - main paper text (note that links to figures are not necessarily all up to date) - main figures and a table - supplementary methods (feel free to add text here) - supplementary figures (tables are not done yet) - legends for supplementary figures and tables (feel free to add text here) We're not there yet, but I can almost see the light at the end of the tunnel... best, Tuuli - Jean: look a bit into classification of sQTL changes - Gabrielle: figure out what will be the stable www address of the wiki - Matthias update splice junction calculations calculate how many splice junctions (out of total) have soft splicing in 1) any individual 2) all individuals. - Micha: Once/if we have the splice junction updates, analyze population frequency / annotation status distribution - Natalja: send supplementary methods text of imputation protocol send supplementary methods text of visualization continue working on visualization tracks - Peter/Irina: analyze repeat eQTL data - Thomas look at editQTLs - Jonas: replot read and gene count histograms - Manny: get numbers of LoF variants (total and covered by RNAseq data) estimate the number of stop+ that are truly NMD - Tuuli (FYI...a lot of work for me...) analyze causal variant discovery and GWAS causal variants run independent eQTL analysis run and plot annotation enrichments of sQTLs plot MDS for peer-corrected mRNA data polish text, legends and a few figures, integrate comments, text and plots from others, add references analyze rare variant mapping if any time remains (unlikely) -- 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, 4 months

[Geuvadis_rna_analysis] analysis group TC November 22

by Tuuli Lappalainen

Hello, Let's have an analysis group call today (22th) at 2pm CET. On the agenda: - action items for the main paper - main paper draft - companion papers 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, 4 months

[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, 5 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, 5 months

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geuvadis_rna_analysis November 2012