geuvadis_rna_analysis May 2012

geuvadis_rna_analysis@lists.crg.es

13 participants
19 discussions

[Geuvadis_rna_analysis] Geuvadis RNAseq abstract for ASHG

by Tuuli Lappalainen

Dear all, Enclosed please find a draft for the abstract that I'm planning to submit on behalf of the Geuvadis RNAseq project for the ASHG meeting in San Francisco. Comments are welcome; please send them by June 4th. The abstract has the maximum allowed number of authors (30) - at least one analyst per group and the PIs. I know there are many others who would deserve to be on that list, and apologies for not being able to include you here. In addition to this main abstract, there will be at least one sub-project abstract that will be sent around later. 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] GEUVADIS RNA Analysis Meeting 2: BARCELONA

by Gabrielle Anne Bertier

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] update to gencode v12

by Tuuli Lappalainen

Hello all, I'd like to update to Gencode v12 gene annotation (Ensembl 67) in the Geuvadis RNAseq project after all. After a lot of discussions, I'm now taking back my last week's decision to stick to v7. That would have made some things easier but others more difficult, and I wouldn't want us to lose any power because of an outdated annotation that might make a bit of a difference especially in the LoF variant annotations. It's not too late to switch yet - we'll need to rerun the transcript quantifications though. We'll let you know when it's done. No one expressed a strong opinion about this before, but if you disagree, please say it now. 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] GEM bams available

by Tuuli Lappalainen

Dear all, Bam files from GEM are now available for download in /upload/geuvadis/wp4_rnaseq/main_project/sequence_data/bam/mrna/gem/ . These are big files so I strongly recommend using aspera; the command for downloading all the files of that folder would be like: cd /my/dir/for/geuvadis/bam/ ~/.aspera/connect/bin/ascp -QT -l 150M -k1 geuvadis@ah01.ebi.ac.uk:/upload/geuvadis/wp4_rnaseq/main_project/sequence_data/bam/mrna/gem/ . (this would create a folder gem/ in /my/dir/for/geuvadis/bam/ and download the files there. -k1 means that it will automatically skip downloading a file again if the name and size matches, which is very useful when you need to restart a download) 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] Geuvadis analysis group TC May 24th

by Tuuli Lappalainen

Hello all, We'll have a Geuvadis analysis group TC today (May 24th) at 2pm CET. On the agenda: - ASHG abstract(s) - wiki and shared writing tools - plans for public sharing of data and documentation - data formats and identifiers - variant annotations - Manny will give an update of LoF analysis - Tuuli will present some slides of ASE analysis (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, 4 months

[Geuvadis_rna_analysis] geuvadis wiki updates: identifiers, formats and ASE

by Tuuli Lappalainen

Hello all, I've written some updates in the Geuvadis wiki: - I've created a page for identifier and file format information. We will all have less grey hair by the end of the project if we are consistent on these things. Please go and update those parts of data that concern you, and let people know of changes also by email - and check this page when creating data files! http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/… - I wrote quite a lot of text about ASE analysis - background information, summary of our pipeline, potential sources of error, available data, and a list of analysis that I'll keep on updating with results later on. http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/… 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] analysis_data/quantification/transcript

by M.Sammeth

Dear all, we just replaced the transcript quantification files in analysis_data/quantification/transcript because we found that a script which counted the number of mapped reads for the RPKM normalization got confused by the whitespace characters inserted by the new casava/Illumina pipeline into the read IDs. Therefore, the RPKM values in the former files were off by ~ factor 2, the exact ratio old/new varies expectedly few % around the median 1.92 (plot attached). Hopefully this lapsus did not affect anybody's work--and please be careful not to run into the same issue when emplyoing programs that split columns by whitespaces on files with these read IDs; that was really a great idea of Illumina. Best, micha -- Dr. Michael Sammeth, GL Functional Bioinformatics Phone: +34-934-020-580, http://www.cnag.eu Centre Nacional d'Anàlisi Genòmica (CNAG), PCB Baldiri Reixac 4-6, Room 02A8, 08028 Barcelona

12 years, 4 months

[Geuvadis_rna_analysis] allelic mapping bias fastqs ready

by Tuuli Lappalainen

Hi all - especially Thasso and Micha, In order to correct/filter for allelic mapping bias in Geuvadis analysis as we've discussed before, I've simulated reads over 1000g variants. The fastq files are available for mapping in /upload/geuvadis/wp4_rnaseq/main_project/external_data/genetic_variation/allelic_mapping_simulation/fastq . These should be mapped with GEM and converted to bam similarly to our real data, except that these are single-end reads. It actually became a lot less reads than I anticipated because I ended up taking only sites that are polymorphic in our populations: it's about 300M reads in total, so I hope that this could be done pretty soon :-) At least, could you please check already this week that the files are OK so that I can modify them if needed without further delay. Further details in the wiki: http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/… 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 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

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geuvadis_rna_analysis May 2012