geuvadis_rna_analysis April 2012

geuvadis_rna_analysis@lists.crg.es

3 participants
8 discussions

[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 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

[Geuvadis_rna_analysis] GEM - BWA comparison results

by Tuuli Lappalainen

Hi all, Here are some slides from the GEM-bwa comparison. 5 samples were mapped with the two mappers, and I analyzed mapping statistics, exon quantifications and allelic ratios. As expected, GEM maps a lot more reads than bwa, and seems to perform very well also otherwise. We can discuss this (and other things) on Thursday's analysis group call (2pm) - I'll send the call details 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, 5 months

[Geuvadis_rna_analysis] Geuvadis ftp and wiki updates

by Tuuli Lappalainen

Dear all, I've updated and reorganized the Geuvadis RNAseq ftp site and wiki. The ftp site now has the following data available (among some additional things): - fastq freezes of both mRNA and miRNA - bwa bam files of all the mRNA data - exon read counts based on bwa mapping - genotypes of the phase1 samples (that don't need imputation) - functional annotation of the genetic variants - sample information sheets and lists of problematic mRNA samples - ASE results with variant annotations (this lacks documentation for now though) Please see the wiki (Data storage section) for further information of the contents of the wiki - those of you uploading data to the ftp, please keep this section of the wiki up to date. The wiki has documentation of what has been done thus far, methods, practical informations and e.g. examples of how to use Aspera, and other information (such as the analysis plan). I'll be in touch with some of you to add data and/or documentation. 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 analysis group TC April 5th - minutes

by Tuuli Lappalainen

Dear all, Here are the minutes of the Geuvadis analysis group TC of Thursday 5th of April. Apologies for the long email, it's been 2 hectic weeks of data processing and we went through a lot of things: Fastq files: - All the labs have uploaded mRNA and miRNA fastqs, except for 48 miRNA samples from Kiel where sequencing was delayed, and a few failed miRNA samples that will be skipped. Checksums are OK. - Kiel will sequence the missing miRNA samples next week - Thasso discovered that labs 2,3,6,7 produced fastq files without reads that fail Illumina quality checks, whereas 1,4,5 had them included - in order to be uniform, they should be filtered from all which has been done by Natalja & Tuuli. Two labs submitted 50bp miRNA reads and Tuuli clipped them. All the new files have been uploaded to the ftp site. - Next week the final set of filtered files, checksums and sample metadata will be put under clear ftp directories as the first raw data freeze - this will still be without more refined QC filters. mRNA data processing - GEM BAM files had format issues and need to be recreated. This is being run for the sandbox dataset, and Tuuli will check that this version is fine before rest of the data is processed. - In order to proceed with the analysis in the meanwhile, Tuuli is finishing mapping with bwa and will start submitting these bams too. The first eQTL and ASE analysis will be based on bwa. - All the mapping result files that were based on nonfiltered data from labs 1,4,5 need to be filtered afterwards - Tuuli and Thasso have taken care of this. - Micha will upload transcript quantifications (RPKM and read counts) to the ftp site, and Tuuli will upload exon read counts - these will happen within a week. - According to Ivo, they are planning to submit the GEM manuscript next week. miRNA data processing - Marc F. has downloaded all the fastqs and started running the first steps of their miRNA pipeline. The basic analysis should be done in 1-2 weeks. Genotypes - Of our 465 samples, 42 are not in 1000g Phase1 dataset and have to be imputed from 2.5M Omni genotypes. Natalja and Thomas W. from Munich had done this in parallel using Impute2. However, Tuuli detected a serious problem in the results - for some reason the imputation quality scores and the allele frequencies are very bad. The imputation will need to be debugged and redone. Tuuli, Thomas and Natalja will look into this next week. The good news is that we can do analysis for now using just the 423 Phase1 samples. Analysis group meeting in Geneva - 19 people will attending. Tuuli presented a draft of the program - first day brainstorming and presentations from all the labs, second day of building a concrete analysis plan with responsibilities and deadlines. Biology of Genomes meeting at Cold Spring Harbor - We got a poster presentation - which is not a bad thing considering the timeline, the meeting is 4.5 weeks. - We went briefly through some main analysis items that we can get done by then at least as first versions: eQTLs and their annotations, ASE, loss-of-function variants, splicing variation, quantitative/qualitative gene expression variation, miRNA variation and miRNA-mRNA correlation, unannotated transcripts... It will be a very nice poster if we work hard. Collaboration with Daniel McArthur (from Boston, previously at Sanger) - Dan is a loss-of-function specialist who has expressed interest in being a collaborator in Geuvadis. We already have analysts who will be working with LoFs and we should make sure that Daniel would do analysis that overlaps with this. However, his expertise in calling putative LoF variants from the 1000g data and pruning out false genotype calls could give us a good additional resource. People were generally positive about including him, and Tuuli will discuss with him in more detail what his interests and contribution would be. That's all for now - happy Easter to everyone! 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, 6 months

[Geuvadis_rna_analysis] Fwd: Geuvadis analysis group meeting in Geneva

by Tuuli Lappalainen

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: Geuvadis analysis group meeting in Geneva Date: Thu, 05 Apr 2012 11:28:49 +0200 From: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch> To: Tuuli.Lappalainen(a)unige.ch, gabrielle.bertier(a)crg.es, olof.karlberg(a)medsci.uu.se, jean.monlong(a)crg.eu, p.a.c.hoen(a)lumc.nl, i.pulyakhina(a)lumc.nl, jonas.carlsson(a)medsci.uu.se, esther.lizano(a)crg.eu, natalja(a)ebi.ac.uk, pedro.ferreira(a)crg.es, marc.friedlaender(a)crg.eu, r.haesler(a)mucosa.de, m.barann(a)ikmb.uni-kiel.de, timstrom(a)helmholtz-muenchen.de, thomas.wieland(a)helmholtz-muenchen.de, thomas.schwarzmayr(a)helmholtz-muenchen.de, sultan(a)molgen.mpg.de, micha(a)sammeth.net, rivas(a)broadinstitute.org CC: Ancilla Stefani <Ancilla.Stefani(a)unige.ch> Hello, Thank you for registering for the Geuvadis analysis group meeting. We'll be 20 people in total, and I'm sure it will be a very productive meeting! Some accommodation practicalities: Hotel Bel Esperance had some rooms available after all, so we decided to accommodate 4 people there - thus far we put Esther, Marc F., Peter and Irina there, but if you prefer Adriatica we can change this. If someone doesn't have accommodation arranged yet: we have one extra room booked at Bel Esperance, and we can give this to you if you let me and/or our admin assistant Ancilla (ancilla.stefani(a)unige.ch) know by April 11. The program draft is below, and we'll discuss it on the analysis group TC today. Please let me know if you have schedule conflicts or other suggestions. This is an informal meeting, so we can also change the times on the fly if needed. I will send a document with the final program and info on practicalities this weekend. best regards, Tuuli Monday, April 16 11 -12 am Geuvadis RNAseq project: Background, aims and data 12 am -12:30 pm Lunch 12:30 -- 2:30pm Presentation by the labs: Ideas, interests, analysis plans and approaches. 10-25 min each + discussion Geneva CNAG Oxford EBI 2:30 -3 pm Coffee 3 -5 pm Presentation by the labs: Kiel Munich CRG Leiden Uppsala Berlin 5 - 5:30 pm Wrap-up 8 pm Dinner at Restaurant Demi-Lune Tuesday, April 17 9 -11:30 am Building an analysis plan 11:30 -12:30 am Lunch 12:30 -- 2:30 pm Building an analysis plan 2:30 -- 3 pm Coffee 3 -- 3:30 pm Wrap-up Questions for Tuesday: -What are the essential analyses that must be done? What else will we do? What are the high-priority analyses? -How do we integrate the different data types? -What kind of data types/formats are needed for the analyses? Sharing of tools and data? -Who will take the lead of each analysis module? Who else wants to be involved/informed? -What are the analyses to do for the Biology of Genomes poster? -Timelines and deadlines -Future meetings -Communication: TCs, mailing lists, wiki, skype -- 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, 6 months

[Geuvadis_rna_analysis] geuvadis TC connection problem

by Tuuli Lappalainen

The call passcode doesn't work for me. Was everyone else able to connect? 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, 6 months

[Geuvadis_rna_analysis] Geuvadis analysis group TC April 5th

by Tuuli Lappalainen

Dear all, We'll have a Geuvadis RNAseq analysis group call on Thursday April 5th at 2pm. Before the call, I'd like to ask you to think what type of data you will need for the first analyses of the Geuvadis RNAseq data. We are very close to finishing data freezes for analysis, and now is the point to identify if additional data types/formats are necessary, and see what can be done to provide these data. On the agenda: - data processing: mRNA, miRNA, sample metadata, genotypes - analysis group meeting program and practicalities (I will send a program draft later) - drafting the outline for the poster/talk at the Biology of Genomes meeting - collaboration with Daniel McArthur best regards, Tuuli The call details: Spain 902 125 136 Other countries +34 91 495 18 99 Participants’ Pin-code: 764989* -- 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, 6 months

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geuvadis_rna_analysis April 2012