geuvadis_rna_analysis

geuvadis_rna_analysis@lists.crg.es

160 discussions

[Geuvadis_rna_analysis] Analysis group TC September 12th

by Tuuli Lappalainen

Hello, We'll have Geuvadis analysis group TC on Thursday 12th of September at 2pm CET. On the agenda: - Analysis updates (see below) - Data visualization and Ensembl collaboration - Pedro will present on differential expression analysis - AOB Call details - different from the usual! Germany +49 692 573 804 41 Netherlands +31 108 920 271 Spain +34 931 816 661 Sweden +46 840 309 949 Switzerland +41 58 262 07 22 United Kingdom +44 203 370 57 19 United States +1 646 381 08 89 /Access code: 611683 / For your information, I have my knee surgery scheduled for this Friday. I'll probably be offline only for a couple of days, but I'm not sure if I'll be able to work that much next week. Thus, if you need some feedback or data from me, let me know now so we can try to sort it out before the surgery. We need to start wrapping up the analysis soon to put the paper together. Thus I'd like to ask you to give brief summary on the stage of your analysis - what you've been doing, are what kind of things are still pending, and when you would be ready to present the result and hand results and text over to me. Below is a list of analyses/people from the paper outline - if your name is there but you won't be on the call, please send the info to the analysis group mailing list before the call. -QC - Jonas, Olof, Peter, Tuuli - Differential expression - Pedro - mRNA qualitative/quantitative variation - Jean, Mar - ASE - Tuuli - Splicing variation - Micha - Soft splicing - Matthias - miRNA-mRNA interactions - Marc, Henk? - RNA editing - Thomas W - Conjoined genes - Liliana - n-TARs - Daniela - Transcription of repeats - Peter/Irina - QTLs - Tuuli - Loss-of-function - Manny - Data visualization - Natalja 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] miRNA sample QC

by Tuuli Lappalainen

Hello, I've done basic QC for miRNA samples. Attached is a sample sheet that denotes samples to use in analysis. From the total 492 samples, 480 samples from 452 unique individuals pass QC. We end up having 705 genes quantified in at least 50% of the samples - most of these have low quantifications though. Analysis of sample correlation and clustering shows even a clearer population clustering than mRNA, and very little lab effects. I've updated the QC section of the wiki with miRNA results: list of samples to exclude, basic read count and mapping stats, and early correlation analysis. The data is on the ftp site: - sample sheet: /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/qc - quantifications: /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/mirna/quantification_tables I'm now running PEER normalization for miRNAs, and that data will probably be the best to use for mRNA-miRNA correlations and eQTL analysis. I'll let you know when this is done. 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

[Geuvadis_rna_analysis] No TC tomorrow

by Tuuli Emilia LAPPALAINEN

Hello, Let's skip tomorrow's Geuvadis analysis group teleconference since there is no presentation scheduled, and it's a public holiday in Geneva. The next one will be on the 13th. best regards, Tuuli

12 years, 1 month

[Geuvadis_rna_analysis] ASE results fixed

by Tuuli Emilia LAPPALAINEN

Dear all, I found a small bug in the ASE results - nothing major, but for any final analysis please use the new file that I uploaded today to the same place as before: /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/ase . Apologies for any extra work that this may have caused. best, Tuuli

12 years, 1 month

[Geuvadis_rna_analysis] important: sample QC updates

by Tuuli Lappalainen

Hello all, IMPORTANT: - sample NA19095.5.M_120131_5 should be excluded from all analyses. This sample is one of the 5 replicates, and for this individual we originally chose another sample (NA19095.2.M_120131_2) to use. Thus, the set of unique 462 samples (which should be used in most analyses) doesn't change. However, if you're analyzing replicates in any way, exclude NA19095.5.M_120131_5. Some more info: Peter did analysis of sex-specific expression, which generally shows very nice clustering to female and male samples. However, 4 samples showed a mixed pattern that is suggestive of cross-contamination. Three of these have been excluded previously due to them showing clear signs of contamination in ASE analysis ( NA12399.7.M_120219_1, NA07000.1.M_120209_2, HG00237.4.M_120208_1). However, the sample NA19095.5.M_120131_5 behaved slightly abnormally in ASE analysis but was not excluded based on that, but the sex-specific analysis shows that this sample needs to be thrown out. Additionally, there are some QC warnings for samples that will be kept in the dataset. In the sex-specific transcription analysis the sample NA11930.3.M_120202_8 behaved slightly abnormally, and Jonas and Olof have also listed samples that are slight outliers based on different statistics. An updated sample information sheet is in the attachment. The UseThisSample flag gives you the set of 462 unique samples (and hasn't changed from the previous file (GD667_mRNA_SampleInformation_270712.txt). Additionally, the QC_OK column denotes all the samples that have passed QC, and QC_Info has information of why a sample failed QC, or QC warnings for QC-passed samples, and these two columns have been updated with the information above. This information can be found in the wiki (http://sanabre.net/geuvadis/index.php/QC_sample_info), and the sample information sheets have been uploaded on the ftp site (/upload/geuvadis/wp4_rnaseq/main_project/analysis_data/qc) 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] 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

← Newer
1
2
3
4
5
6
7
8
9
...
16
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

geuvadis_rna_analysis