geuvadis_rna_analysis

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160 discussions

[Geuvadis_rna_analysis] basic miRNA analyses uploaded

by Marc Friedlaender

Hello, as Tuuli mentioned, I have uploaded the results of the basic miRNA analyses to the ebi server at: ftp://ftp-private.ebi.ac.uk/upload/geuvadis/wp4_rnaseq/main_project/analysis_data/mirna/ There is a README file which supplies description of files and methods. I will lift the README to the wiki tomorrow. The analyses include phred scores, clipped reads, mappings, annotation breakdowns and summary statistics. cheers, Marc Marc Friedländer, Ph.D. Xavier Estivill laboratory Genes and Disease programme Centre for Genomic Regulation (CRG) C/ Dr. Aiguader, 88 08003 Barcelona, Spain Phone: +34 933160203

12 years, 1 month

[Geuvadis_rna_analysis] Analysis group TC August 23rd

by Tuuli Lappalainen

Hello, We'll have a Geuvadis RNAseq analysis group TC on Thursday August 23rd at 2pm. On the agenda: - the next analysis group meeting - presentation by Matthias about soft splicing (probably, if the phone system of their new building allows him to call in) - 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] No analysis group TC on the 15th

by Tuuli Lappalainen

Dear all, Let's cancel the Geuvadis analysis group TC that we had planned for tomorrow, August 16th, due to vacation time and other obstacles. The next call will be on Thursday August 23th. 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, 2 months

[Geuvadis_rna_analysis] analysis group face-to-face meeting

by Tuuli Lappalainen

Hello, We need to decide if we want to organize a third Geuvadis RNAseq analysis group face-to-face meeting, and if yes, where and when this would be. I put together a small poll - please reply by Friday 24th of August: https://docs.google.com/spreadsheet/viewform?formkey=dGhhRkVCSllrNEdTYVlSZ3… 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, 2 months

[Geuvadis_rna_analysis] Analysis group TC on Aug 9th

by Tuuli Lappalainen

Hello all, We'll have a Geuvadis analysis group call on Thursday August 9th at 2pm as usual. Apologies for the late notice. On the agenda: - The new wiki - The (possible) third analysis group meeting next fall - I'll present some slides about QC and technical covariates - AOB We'll continue discussing the QC companion paper with Peter et al. after the main 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, 2 months

[Geuvadis_rna_analysis] Geuvadis RNAseq poster at ASHG

by Tuuli Lappalainen

Dear all, For you information, the Geuvadis RNAseq abstracts didn't unfortunately get accepted as platform presentations at the ASHG meeting in San Francisco - I will be presenting a poster on the main project, and Manny Rivas will also have a poster on loss-of-function analyses. 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 -------- Original Message -------- Subject: ASHG 2012: Abstract Assignment/Programming Information Poster Authors Date: Tue, 31 Jul 2012 11:02:09 -0400 From: ASHG Meetings <ashgmeetings(a)ashg.org> Organization: The American Society of Human Genetics To: Tuuli.Lappalainen(a)unige.ch ASHG EMAIL <http://www.ashg.org/cgi-bin/rda.pl?u=100&e=1080> July 31, 2012 Dear Tuuli Lappalainen: This confirms your abstract has been ACCEPTED for a *POSTER* presentation at the 62nd American Society of Human Genetics Annual Meeting in San Francisco, California, November 6-10, 2012. _Please review all information in this email as it contains important details of your assignment_. Please print and bring this e-mail with you to the meeting. _*Accessing Your Poster Assignment*_ You may access your poster presentation assignment day and time by clicking on Abstract Assignment <http://www.ashg.org/cgi-bin/rda.pl?u=101&e=1080> on the ASHG 2012 Web site. All poster presentations will take place inside the Moscone Center, Exhibit Halls ABC on the Lower Level. *We do not accept requests to change the day of presentation* and it is no longer possible to withdraw your abstract. If you are *unable to present* on the day assigned, please ask a co-author or colleague to present on your behalf and notify the ASHG Management Office at ashgmeetings(a)ashg.org <mailto:ashgmeetings@ashg.org> of the presenter change so that a notation can be included in the program addendum. *_Program/Abstract/Board Number:_* The letters *W*, *T*, or *F* of the program/abstract/board number indicates the day (i.e., _W_ednesday, _T_hursday or _F_riday) on which authors present their work. The number indicates the board you are to use for displaying your poster. Posters should remain on the boards for all three days. *_Abstract Availability_* Your abstract and all other 2012 Annual Meeting abstracts will be available to view via the Abstract Search Program on the ASHG 2012 Web site on/after September 6, 2012. *_Registration and Housing_* All poster presenters are required to register for the meeting. If you have not yet registered or made hotel reservations, click on the links below. Registration <http://www.ashg.org/cgi-bin/rda.pl?u=102&e=1080> Hotel Reservations <http://www.ashg.org/cgi-bin/rda.pl?u=103&e=1080> Room Sharing/Bulletin Board <http://www.ashg.org/cgi-bin/rda.pl?u=104&e=1080> *_Poster Mounting and Removal_* *Authors must put up and take down their posters according to the schedule below.* Authors must be present at their boards based on their odd and even abstract/program/board number, and must remain at their boards for the duration of their scheduled presentation times. Posters should remain on the boards for all three days. *Wednesday, November 7* 10:00 am–10:30 am All poster authors (Wednesday, Thursday and Friday) place posters on boards _Note_: Posters should remain on the boards for all three days. 10:00 am–4:30 pm Posters available for general viewing *2:15 pm–4:15 pm* *Poster Session I (_W_ednesday Authors Present) * *2:15 pm–3:15 pm (/odd poster board numbers; author must be present/)* *3:15 pm–4:15 pm (/even poster board numbers; author must be present/)* *Thursday, November 8* 7:00 am–4:30 pm Posters available for general viewing *2:15 pm–4:15 pm* *Poster Session II (_T_hursday Authors Present) * *2:15 pm–3:15 pm (/odd poster board numbers; author must be present/)* *3:15 pm–4:15 pm (/even poster board numbers; author must be present/)* *Friday, November 9* 7:00 am–4:30 pm Posters available for general viewing *2:15 pm–4:15 pm * *Poster Session III (_F_riday Authors Present) * *2:15 pm–3:15 pm (/odd poster board numbers; author must be present/)* *3:15 pm–4:15 pm (/even poster board numbers; author must be present/)* 4:15 pm – 4:30 pm All authors remove posters from boards /You will not have access after 4:30 pm to take down your poster./ 4:30 pm Exhibit Hall and Posters closed. *_Preparation for your Poster Presentation_ * Each poster author will be assigned to _share a poster board_. Each author will have a net useable space in portrait/vertical format that measures _2'10" (86.36 cm) wide x 3'8" (111.76 cm) high_. When creating your poster, please use these dimensions. Please read the _Instructions for Authors of Posters <http://www.ashg.org/cgi-bin/rda.pl?u=105&e=1080>_ and then follow the _Guidelines for Preparing Effective Posters/Poster Size <http://www.ashg.org/cgi-bin/rda.pl?u=106&e=1080>_. *_Important Presenter Information_* * ASHG _requires disclosure of gene names_ as part of your presentation and sharing research data so that findings can be replicated and other investigators with similar data can test findings against their own. Authors who do not provide gene names at the meeting will be subject to sanctions as determined by the Program Committee. * When presenting data and health information (including photos) all presenters must have informed consent compliant with human subjects and applicable HIPAA regulation. * Authors must disclose on their poster whether the abstract has been previously published (prior to November 2012). If the abstract has been previously published, authors should indicate the date and publication. * When preparing your poster, please check the poster size guidelines before printing (see above). * You must register and wear an official ASHG 2012 scientific meeting badge to gain admittance at any time to the poster areas. Unregistered guests (i.e., friends, co-workers, etc.) are not permitted to attend the poster sessions. * All poster boards will be pre-numbered. Please be certain to mount your poster on the correct board. * Remember to bring your own pushpins (in your checked luggage). We will have a very limited number of pushpins available at the meeting. * Do not leave personal materials or belongings under poster boards or in the poster area. ASHG is not responsible for any articles left in the poster area or elsewhere. * There is _no access to the Exhibit Hall_ before 10:00 am on Wednesday or after 4:30 pm on Friday. * Click HERE <http://www.ashg.org/cgi-bin/rda.pl?u=107&e=1080> for a suggested format for _abstract citation._ *_Camera/Recording Policy _* Attendees are _strictly prohibited_ from using cameras and all other recording devices on the Exhibit Hall floor, and in all poster/oral presentations. This means that attendees are _not_ permitted to take pictures or videos of speaker slides, posters or exhibit booths. Attendees not adhering to this policy may be asked to leave the room and will be asked to delete all pictures or videos already taken, and further action may be taken with repeated or egregious offenders. When registering, you indicated that would adhere to this policy. *_Poster Printed, Laminated and Ready for Pickup at the Meeting_ Deadline October 2, 2012* You have the option of printing your poster for pickup when you arrive in San Francisco. A separate e-mail will be sent to poster authors about this service by Mira Digital Printing. You can also e-mail the company directly at ASHG2012(a)mirasmart.com <mailto:ASHG2012@mirasmart.com>. The cost is $50 per poster, plus $25 shipping and the deadline for uploading your poster files is October 2, 2012. We look forward to your participation in the 62nd Annual Meeting of the American Society of Human Genetics. For questions, please contact the ASHG Management Office at ashgmeetings(a)ashg.org <mailto:ashgmeetings@ashg.org>. Sincerely, Joann A. Boughman, PhD Executive Vice President American Society of Human Genetics

12 years, 2 months

[Geuvadis_rna_analysis] qc paper

by P.A.C._t_Hoen＠lumc.nl

Dear all I updated the doc on the lay-out of the qc paper based on yesterday's discussion. I attach it and also modified the section on the wiki Best Peter Dr. Peter A.C. 't Hoen Center for Human and Clinical Genetics Leiden University Medical Center Postal zone S4-P PO Box 9600 2300 RC Leiden The Netherlands phone: +31-71-5269421 fax: +31-71-5268285 e-mail: p.a.c.hoen(a)lumc.nl

12 years, 2 months

Re: [Geuvadis_rna_analysis] Analysis group TC on Aug 9th

by Tuuli Lappalainen

...and here are the slides... 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 8/9/12 1:37 PM, Jonas Carlsson wrote: > You forgot the slides ... > /Jonas > > On 08/09/2012 01:34 PM, Tuuli Lappalainen wrote: >> Here are my slides for today's call. >> >> I forgot the call details from the previous email: >> >> 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 >> >> On 8/8/12 11:33 PM, Tuuli Lappalainen wrote: >>> Hello all, >>> >>> We'll have a Geuvadis analysis group call on Thursday August 9th at 2pm >>> as usual. Apologies for the late notice. >>> >>> On the agenda: >>> - The new wiki >>> - The (possible) third analysis group meeting next fall >>> - I'll present some slides about QC and technical covariates >>> - AOB >>> >>> We'll continue discussing the QC companion paper with Peter et al. >>> after >>> the main call. >>> >>> best regards, >>> Tuuli >>> >> _______________________________________________ >> Geuvadis_rna_analysis mailing list >> Geuvadis_rna_analysis(a)lists.crg.es >> http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis >

12 years, 2 months

[Geuvadis_rna_analysis] New Geuvadis wiki

by Tuuli Lappalainen

Hello all, The new Geuvadis wiki is now functional, and can be accessed in http://sanabre.net/geuvadis. Your personal user names can be found in the attached file, and the password is 'franciscrick'. I've only taken a quick look at the new wiki, but it looks a lot better, seems to be more flexible and is easier to use. I'll be doing a bunch of updates and maintenance during this week. If you have further questions, comments or requests, feel free to email me and/or Gabrielle. 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 -------- Original Message -------- Subject: FW: Geuvadis MediaWiki e-mail address confirmation Date: Fri, 03 Aug 2012 17:10:49 +0200 From: Gabrielle Anne Bertier <gabrielle.bertier(a)crg.eu> To: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch> CC: Michael Sammeth <micha(a)sammeth.net> Hi Tuuli, normally it should be better now. whenever you judge it good enough you can send the access to all participants. (usernames attached) I'm going on holidays now but I'll be connected, if you have more comments I can pass it on to the company, but I think we can start working with this new version ! If so let me know and I'll de activate the old version of the Wiki Thanks ! Ciao, Gabrielle Wiki link: http://sanabre.net/geuvadis. Usernames attached password: 'franciscrick'

12 years, 2 months

[Geuvadis_rna_analysis] OPS transformation (Micha) followed by Pearson correlation

by P.A.C._t_Hoen＠lumc.nl

Dear all We are all aware of the pitfalls of Pearson correlations on largely skewed data. Micha mentioned in Barcelona the OPS (optimal power space transformation package) that he developed. It worked very well to determine correlations between samples, I believe. Attached some results. Best Peter Dr. Peter A.C. 't Hoen Center for Human and Clinical Genetics Leiden University Medical Center Postal zone S4-P PO Box 9600 2300 RC Leiden The Netherlands phone: +31-71-5269421 fax: +31-71-5268285 e-mail: p.a.c.hoen(a)lumc.nl

12 years, 2 months

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