geuvadis_rna_analysis June 2012

geuvadis_rna_analysis@lists.crg.es

14 participants
17 discussions

[Geuvadis_rna_analysis] analysis group TC June 28th

by Tuuli Lappalainen

Hello, We'll have a Geuvadis analysis group TC on Thursday 28th at 2pm CET. On the agenda: - analysis updates - wiki - Liniana's presentation: "Conjoined genes in human populations" - Mar's presentation: "Ubiquity vs specificity of gene and isoform expression across populations" NOTE: Call details different from the usual: Germany: 0049 692 573 804 41 Spain: 0034 931 816 661 UK: 0044 203 370 57 19 Sweden: 0046 840 309 949 The Netherlands: 0031 108 920 271 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, 3 months

[Geuvadis_rna_analysis] Fwd: Analysis group TC June 21st

by Mar Gonzàlez-Porta

Mar ---------- Forwarded message ---------- From: Mar Gonzàlez-Porta <mar(a)ebi.ac.uk> Date: 2012/6/21 Subject: Re: [Geuvadis_rna_analysis] Analysis group TC June 21st To: Natalja Kurbatova <natalja(a)ebi.ac.uk> Cc: Liliana Greger <lgreger(a)ebi.ac.uk> Please find attached the slides for today's meeting. Cheers, Mar 2012/6/20 Natalja Kurbatova <natalja(a)ebi.ac.uk> > > > -------- Original Message -------- Subject: [Geuvadis_rna_analysis] > Analysis group TC June 21st Date: Wed, 20 Jun 2012 16:26:36 +0200 From: Tuuli > Lappalainen <Tuuli.Lappalainen(a)unige.ch> <Tuuli.Lappalainen(a)unige.ch> To: > geuvadis_rna_analysis(a)lists.crg.es <geuvadis_rna_analysis(a)lists.crg.es><geuvadis_rna_analysis(a)lists.crg.es> > > Hello all, > > We'll have a Geuvadis RNAseq analysis group TC on Thursday June 21st at > 2pm CET. > > On the agenda: > - program for the Barcelona meeting (see attached draft) > - data and analysis updates > - Jonas from Uppsala will present some QC results > - Liliana from EBI will present "Conjoined genes in human populations" > - Mar from EBI will present "Ubiquity vs specificity of gene and isoform > expression across populations" (if there's time) > > Call details are: > from outside spain; 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)22-3795550tuuli.lappalainen(a)unige.ch > >

12 years, 3 months

[Geuvadis_rna_analysis] Conjoined Genes in human populations

by Liliana Greger

Hello All, Please find attached the updates slides which I will present on the today's conference call. Regards Liliana Dr. Liliana Greger EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD

12 years, 3 months

[Geuvadis_rna_analysis] Analysis group TC June 21st

by Tuuli Lappalainen

Hello all, We'll have a Geuvadis RNAseq analysis group TC on Thursday June 21st at 2pm CET. On the agenda: - program for the Barcelona meeting (see attached draft) - data and analysis updates - Jonas from Uppsala will present some QC results - Liliana from EBI will present "Conjoined genes in human populations" - Mar from EBI will present "Ubiquity vs specificity of gene and isoform expression across populations" (if there's time) Call details are: from outside spain; 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, 3 months

[Geuvadis_rna_analysis] slides for today

by Natalja Kurbatova

Here are slides for today's conference call from Liliana. Regards, Natalja

12 years, 3 months

[Geuvadis_rna_analysis] Conjoined genes in human populations - slides

by Liliana Greger

Dear All, These are the slides for the Geuvadis meeting today. Regards Liliana Dr. Liliana Greger EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD

12 years, 3 months

[Geuvadis_rna_analysis] Analysis group TC June 7th

by Tuuli Lappalainen

Hello all, We'll have a Geuvadis analysis group call on Thursday June 7th at 2PM CET. On the agenda: - Barcelona meeting arrangements - data updates: quantifications, genotypes, annotations - updates from subgroup analyses - Tuuli will present slides of allele-specific expression analysis Call details are: from outside spain; 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, 4 months

Re: [Geuvadis_rna_analysis] GEM .bam-files does not have headers

by Tuuli Lappalainen

Hello, Jonas pointed out that the GEM bam files don't have header lines, which may be a problem in some cases. I uploaded a reference index file (/upload/geuvadis/wp4_rnaseq/main_project/external_data/reference/hg19_AXYM.fa.fai) that can be used at least in samtools as additional information so that header info is not required, or you can also use that to add headers to your bams if you like. 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 On 6/18/12 11:29 AM, Jonas Carlsson wrote: > Hello! > > When I tried to run QC-analysis on the GEM-files many of the analysis > modules failed because there is no header in the .bam-files. Is this a > mistake or by choice? > > /Jonas

12 years, 4 months

[Geuvadis_rna_analysis] Geuvadis genotypes available

by Tuuli Lappalainen

Hello all, The Geuvadis RNAseq genotypes from Phase1 and Phase2 samples are now available in: /upload/geuvadis/wp4_rnaseq/main_project/external_data/genetic_variation/genotype/phase1_phase2/ These are vcf files, with a .genotypes.vcf file per chromosome, and a .sites.vcf file of the whole genome that contains the first 8 columns of the genotype files with all the variant information. See the header lines for explanation of the info tags. There's also a sample information file. In a couple of weeks there will be an update on the variant annotations. Phase1 genotypes come from 1000g Phase1 v3 release, and Phase2 genotypes have been imputed from Omni2.5M - wiki has some more details on this from Natalja. The imputation results have been filtered as follows; in the end we have 38,187,570 variants left. - imputed Phase2 genotypes with bad imputation quality (<0.5) have missing values. Note that Phase1 genotypes for these variants are perfectly OK to use in analyses even though the overall missingness rate is 10%. - variants with multiple alleles and sites with multiple variants have been excluded. I noticed that either imputation or the merge of the Phase1 and Phase2 data messed up some of these sites, so I thought that the safest thing to do is to remove them - it's not a huge loss and I'm not sure how reliable these genotype calls are in the Phase 1 anyway. - Even after these filters, there was a very low number of variants with very discordant frequencies in Phase1 and Phase2. Most of these seemed to be variants that are on the Omni2.5M with an allele flip in the original Phase2 SNP genotypes data that was used in imputation. This is an ad hoc filter, but I removed 2876 variants with >0.3 frequency difference between Phase1 and Phase2. I've done a number of checks on these files, but please let me know if you observe anything that doesn't seem right. Thanks to Natalja and Thomas W for all the work for getting these data together. 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, 4 months

[Geuvadis_rna_analysis] no analysis group TC on the 14th

by Tuuli Lappalainen

Hello all, Let's skip this week's Geuvadis RNAseq analysis group TC - the next call will be in one week, on June 21st at 2pm CET. 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, 4 months

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

geuvadis_rna_analysis June 2012