geuvadis_rna_analysis

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160 discussions

[Geuvadis_rna_analysis] Geuvadis RNAseq analysis group TC May 17th

by Tuuli Lappalainen

Hello, We'll have a Geuvadis analysis group TC on Thursday the 17th at 2pm CET. I know this is a public holiday in many countries, but I'd prefer having the call anyway with those of you who can attend, it's been a while. Things to discuss: - updates from GEM submission and bams, QC, and imputation - reference allele mapping bias simulations for GEM - next steps in analysis: - eQTL tests - splice junction quantifications - variant annotation categories - miRNA - loss-of-function - others? - July meeting practicalities The numbers are: from outside spain; 0034917911859 from spain; 900800678 Access code; 3160100 -- 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] poster prize for Geuvadis RNAseq project

by Tuuli Lappalainen

Dear all, I already told the Geuvadis RNAseq analysis group that our poster at the Biology of Genomes meeting was very popular - in addition to that, on the last day of the meeting it was announced to be one of the poster prize winners! Thanks again for all of you for your contribution thus far. I'm now even more motivated than before to continue the work to meet the high expectations for our project. 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, 5 months

[Geuvadis_rna_analysis] Geuvadis updates from Cold Spring Harbor

by Tuuli Lappalainen

Hello all, Greetings from Cold Spring Harbor! The Geuvadis RNAseq poster was really popular and lots of people were impressed by the dataset and the analyses that we put together for the poster. There is definitely a lot of interest in the paper and the dataset. Now that there are so many people waiting for the paper and the data to come out, let's keep on working to make sure we'll get it done sooner rather than later. A couple of questions/issues: - FYI to everyone, the GEM manuscript is still not submitted despite many promises to get it done by the end of April. - Micha/Thasso, what's the situation regarding the gem-bam conversions? Are you running them and if not, can you start asap? We need to make sure that if the manuscript gets submitted and we can decide to use GEM (I wish that this was a question of when and not if), there's no delay from this. - genotype data of the Phase2 samples: I talked with Bryan Howie (developer of IMPUTE2), and he said that including rare variants and indels in the reference panel should be fine. Natalja/Thomas, am I correct that we already had chr1 results where imputation was done with the full Phase2 set + the total Phase1 without any additional variant filters, and this looked pretty good? On another note, I learned that the Phase2 genotype calls are almost there - I'm discussing with people from the Broad if we could use them and if that would give us better data than imputing. 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, 5 months

[Geuvadis_rna_analysis] Reorganizing QC section of the wiki

by Tuuli Lappalainen

Hello, I've added material of the QC analysis that I've done thus far to the wiki. The pages needs some reorganization right now to get the old material in places that make sense. Olof and Jonas, can you go to the wiki QC page and see if the structure that I'm suggesting there makes sense to you? If you don't object, Gabrielle, could you do the following moves and renames: - Analysis/Normalization of quantifications -> Analysis/QC/QC analysis/Normalization of quantifications - Analysis/QC/ DNA contamination <http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/…> -> Analysis/QC/QC analysis/DNA contamination <http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/…> - Analysis/QC/ Epstein-Barr virus activity <http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/…><http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/…> -> Analysis/QC/QC analysis/Epstein-Barr virus activity <http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/…> - Analysis/QC/ Small RNA QC <http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/…> -> Analysis/QC/QC analysis/Small RNA QC <http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/…> stats - Analysis/QC/RNA quality <http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/…> -> Analysis/QC/QC analysis/RNA quality data Additionally, Gabrielle, could you see if the wiki could be made to scale figures better? I inserted some png figures that show up on my screen as really big, and one needs to scroll the page up and down and sideways to see them. It's a pain if we need to manually resize figures before uploading. And the Presentations page is still missing (it got deleted by accident), how's the recovery process going? 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, 5 months

[Geuvadis_rna_analysis] Geuvadis analysis group TC May 3rd

by Tuuli Lappalainen

Hi all, We'll have a Geuvadis RNAseq analysis group TC on Thursday May 3rd at 2pm. On the agenda: - Tuuli will present the Biology of Genomes poster - Other analysis updates - Steps needed to get a final freeze for analysis by the end of May - Analysis group meeting in Barcelona - Mailing lists Call details: Spain 902 125 136 Other countries +34 91 495 18 99 <tel:%2B34%2091%20495%2018%2099> Participants' Pin-code: 764989* 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, 5 months

[Geuvadis_rna_analysis] Geuvadis RNAseq analysis group meeting July 9-10

by Tuuli Lappalainen

Dear all, We will have the next Geuvadis analysis group meeting in Barcelona in July 9-10. More info will follow around the end of May. 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, 5 months

[Geuvadis_rna_analysis] Biology of genomes poster - latest version

by Tuuli Lappalainen

Hi all, Here's the latest version of the poster to discuss on the call. 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, 5 months

[Geuvadis_rna_analysis] GEUVADIS RNAseq General Update - 26.04.2012 - 11am

by Gabrielle Anne Bertier

Dear All, thank you very much for filling in the doodle. We'll have the next TC on Thursday 26th April at 11am Date and time Thursday 26th April at 11am Ready-Access Number: 900800678 Secondary Ready-Access Number: +34 917911859 7-Digit Access Code: 3160100 Tentative agenda: - status of the data - updates from the analysis group meeting - analysis plans - Biology of Genomes poster draft - future meetings The next Analysis meeting will take place in Barcelona and anyone interested is welcome to join, here is the doodle for the next meeting: http://www.doodle.com/z7a3mq92b9syz9xg Conference code: Best, Tuuli and Gabrielle Gabrielle Bertier Scientific Project Manager International Collaboration Office 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 From: geuvadis_wpl-bounces(a)lists.crg.es [mailto:geuvadis_wpl-bounces@lists.crg.es] On Behalf Of Tuuli Lappalainen Sent: 17 April, 2012 5:22 PM Cc: geuvadis_rnaseq(a)lists.crg.es; geuvadis_wpl(a)lists.crg.es Subject: Re: [Geuvadis_wpl] GEUVADIS RNAseq General Update Dear all, Please fill in the Doodle for a TC with the whole Geuvadis RNAseq group by Wednesday noon. 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<mailto:tuuli.lappalainen@unige.ch> On 4/12/12 11:10 AM, Gabrielle Anne Bertier wrote: Dear all, At the request of Tuuli, please fill in the doodle<http://doodle.com/3i5f4wt28ez596sx> to schedule a TC with the whole RNAseq group for an update on the data analysis. Tentative agenda: - status of the data - updates from the analysis group meeting - analysis plans - Biology of Genomes poster draft - future meetings Kind regards, Gabrielle doodle full link: http://doodle.com/3i5f4wt28ez596sx Gabrielle Bertier Scientific Project Manager International Collaboration Office 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 _______________________________________________ Geuvadis_wpl mailing list Geuvadis_wpl(a)lists.crg.es<mailto:Geuvadis_wpl@lists.crg.es> http://davinci.crg.es/mailman/listinfo/geuvadis_wpl

12 years, 5 months

[Geuvadis_rna_analysis] Geuvadis RNAseq poster for Biology of Genomes

by Tuuli Lappalainen

Dear all, Enclosed please find a draft of the Geuvadis RNAseq poster that I'll be presenting next week at the Biology of Genomes meeting in Cold Spring Harbor. Small changes are still possible until Thursday, so comments are welcome. I think we managed to put together some pretty cool results in a very short time - my special thanks go to Micha, Marc F, Jean and Manny for contributing results and figures for the poster. 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, 5 months

[Geuvadis_rna_analysis] Geuvadis RNAseq next analysis group meeting - fill the doodle

by Tuuli Lappalainen

Dear all, The next Geuvadis analysis group meeting will take place in Barcelona in late June or early July. If you'd be interested in attending, please fill the Doodle to find the best time for the 2-day meeting: http://www.doodle.com/z7a3mq92b9syz9xg 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, 5 months

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