geuvadis_rna_analysis

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160 discussions

[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, 4 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

[Geuvadis_rna_analysis] DEADLINE TODAY - GEUVADIS RNA Analysis Meeting 2: BARCELONA

by Gabrielle Anne Bertier

Gentle reminder Please register today ! Gabrielle Registration form full link: https://docs.google.com/spreadsheet/viewform?pli=1&formkey=dDFxZ2diT0hUVFhu… From: Gabrielle Anne Bertier Sent: 05 June, 2012 10:04 AM To: 'geuvadis_rna_analysis(a)lists.crg.es'; 'geuvadis_rnaseq(a)lists.crg.es' Cc: 'geuvadis_wpl(a)lists.crg.es'; Xavier Estivill; Michela Bertero; 'Tuuli Lappalainen'; Magali Bartomeus Cistare Subject: REMINDER: GEUVADIS RNA Analysis Meeting 2: BARCELONA Dear all, please remember to register for the meeting before this Friday ! Gabrielle Registration form full link: https://docs.google.com/spreadsheet/viewform?pli=1&formkey=dDFxZ2diT0hUVFhu… From: Gabrielle Anne Bertier Sent: 30 May, 2012 1:20 PM To: geuvadis_rna_analysis(a)lists.crg.es<mailto:geuvadis_rna_analysis@lists.crg.es>; geuvadis_rnaseq(a)lists.crg.es<mailto:geuvadis_rnaseq@lists.crg.es> Cc: geuvadis_wpl(a)lists.crg.es<mailto:geuvadis_wpl@lists.crg.es>; Xavier Estivill; Michela Bertero; 'Tuuli Lappalainen'; Magali Bartomeus Cistare Subject: GEUVADIS RNA Analysis Meeting 2: BARCELONA Dear all, Please find here the registration form<https://docs.google.com/spreadsheet/viewform?pli=1&formkey=dDFxZ2diT0hUVFhu…> for the 2nd GEUVADIS RNA analysis meeting; which will take place at the CRG in Barcelona; on:. Monday July 9th; from 12:00 to 17:00 Tuesday July 10th; from 09:00 to 16:00. A detail agenda will follow soon. Please forward this to any relevant person in your lab. Registration deadline: 8th June 2012 The hotel has to be paid from your own GEUVADIS budget. We have pre-booked 30 hotel rooms for the 9th of July near the CRG; in: Hotel H10 Marina<http://www.hotelh10marinabarcelona.com/en/index.html> Hotel H4<http://www.besthotelscities.com/hotel4barcelona/index.php> If you want to stay for more nights, or in a different hotel please tick the according box in the registration form, and we'll provide you with hotel suggestions. Registration form full link: https://docs.google.com/spreadsheet/viewform?pli=1&formkey=dDFxZ2diT0hUVFhu… Don't hesitate to contact me in case you have any question, 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, 4 months

[Geuvadis_rna_analysis] transcript quantifications available

by Tuuli Lappalainen

Hello, Geuvadis mRNA transcript quantifications from flux are now available in: /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/quantification/transcript There are both individual gtf files, and tab-separated tables of reads and rpkms in all the samples. 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

[Geuvadis_rna_analysis] data needed for analysis

by Tuuli Lappalainen

Dear all, Something that I'd like you think/discuss a bit in advance before the Geuvadis analysis call today: Are there data, resources, or general information that are still lacking and that you(r group) needs in order to proceed with the analysis that you have planned? We'll discuss on the call how and when we'll be able to have everything set for people to work on their analysis. 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

[Geuvadis_rna_analysis] REMINDER: GEUVADIS RNA Analysis Meeting 2: BARCELONA

by Gabrielle Anne Bertier

Dear all, please remember to register for the meeting before this Friday ! Gabrielle Registration form full link: https://docs.google.com/spreadsheet/viewform?pli=1&formkey=dDFxZ2diT0hUVFhu… From: Gabrielle Anne Bertier Sent: 30 May, 2012 1:20 PM To: geuvadis_rna_analysis(a)lists.crg.es; geuvadis_rnaseq(a)lists.crg.es Cc: geuvadis_wpl(a)lists.crg.es; Xavier Estivill; Michela Bertero; 'Tuuli Lappalainen'; Magali Bartomeus Cistare Subject: GEUVADIS RNA Analysis Meeting 2: BARCELONA Dear all, Please find here the registration form<https://docs.google.com/spreadsheet/viewform?pli=1&formkey=dDFxZ2diT0hUVFhu…> for the 2nd GEUVADIS RNA analysis meeting; which will take place at the CRG in Barcelona; on:. Monday July 9th; from 12:00 to 17:00 Tuesday July 10th; from 09:00 to 16:00. A detail agenda will follow soon. Please forward this to any relevant person in your lab. Registration deadline: 8th June 2012 The hotel has to be paid from your own GEUVADIS budget. We have pre-booked 30 hotel rooms for the 9th of July near the CRG; in: Hotel H10 Marina<http://www.hotelh10marinabarcelona.com/en/index.html> Hotel H4<http://www.besthotelscities.com/hotel4barcelona/index.php> If you want to stay for more nights, or in a different hotel please tick the according box in the registration form, and we'll provide you with hotel suggestions. Registration form full link: https://docs.google.com/spreadsheet/viewform?pli=1&formkey=dDFxZ2diT0hUVFhu… Don't hesitate to contact me in case you have any question, 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, 4 months

[Geuvadis_rna_analysis] miRNA sequencing

by Daniela Esser

Dear all, The sequencing of the miRNA is finished in Kiel and the fastq files are now available for download in /upload/geuvadis/wp4_rnaseq/main_project/sequence_data/fastq/mirna/ best regards Daniela -- Daniela Esser Institute of Clinical Molecular Biology Christian Albrechts University Kiel Schittenhelmstr. 12 D-24105 Kiel, Germany d.esser(a)ikmb.uni-kiel.de office: +49 - (0)431-5978681

12 years, 4 months

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