geuvadis_rna_analysis

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160 discussions

[Geuvadis_rna_analysis] Geuvadis QC skype call on Wednesday morning

by Tuuli Lappalainen

Hello all, Apologies for the extremely late notice, but there's a skype call on Wednesday morning at 9am CET to discuss quality control analyses (with at least myself, Olof, Jonas and Marc F attending). Feel free to join if you like, and get this message on time. I completely forgot to tell about this before, sorry about that. We'll have the normal analysis group TC on Thursday at 2pm, I'll send a separate email about that. 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

[Geuvadis_rna_analysis] FTP site

by Natalja Kurbatova

Hi, Our systems group has done FTP accounts synchronization. The last step is smth called "the final merge". They have to disconnect both accounts in order to accomplish it. *Monday morning from 8AM till 11 AM our Geuvadis FTP sites will be not available. * After that time everything should work as normal: - the *same login details* as it was before - *both Aspera and FTP* connections are supported Regards, Natalja -- Natalja Kurbatova, PhD Functional Genomics Group, EBI

12 years, 6 months

[Geuvadis_rna_analysis] Geuvadis analysis group TC March 22 - Minutes

by Tuuli Lappalainen

Dear all, Here are the minutes of the Geuvadis RNAseq analysis group call of March 20. The next call will be in two weeks, April 5th. *Action items: *- Berlin should upload the miRNA sample information sheet to the ftp site asap - People should send Mathias from Uppsala the RNA quality info that he has asked for - Those who want to present on a specific topic at the analysis group meeting should email Tuuli - Everyone who wants to be involved in miRNA analysis should send Esther (esther.lizano(a)crg.es) an email Data submissions - All mRNA data is submitted. Tuuli will go through all the files, checksums and sample info for a final fastq freeze. - All the miRNA data has been submitted except for Kiel that had sequencer issues and Munich that postponed the run. We'll proceed with the analysis of the data that we have thus far (Tuuli will check these files and sample info as well), and add these missing ~100 samples later. - Mathias from Uppsala needs RNA quality data of the 5 replicate samples - please send it to him Analysis group meeting - Tuuli will put together a preliminary program. Those who want to present on a specific topic should send Tuuli an email, otherwise / in addition there will be 45-60min slots for all the labs to talk about analysis that they've done/planned. We'll brainstorm the first day and put together a practical analysis plan on the second day. miRNA processing - the Barcelona miRNA pipeline will be used to process (map, quantify) the miRNAs. They'll start downloading the data as soon as possible. Tuuli prepare the alternative allele miRNA reference sequences - People who want to be involved in the miRNA analysis should let Esther know mRNA processing - Micha presented their pipeline for mapping and quantification. The mapping statistics of Geuvadis samples look good, no huge lab effects. - the fact that GEM isn't published yet is a problem, and in Manolis's opinion we should use another mapper if the manuscript is not submitted by the end of April. Thus far we'll work with the GEM bams, but Tuuli will check with Natalja if EBI could map everything with bwa as a precaution. 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, 7 months

[Geuvadis_rna_analysis] Geuvadis analysis group TC March 22

by Tuuli Lappalainen

Hello, We'll have a Geuvadis analysis group call on Thursday (March 22) at 2pm. On the agenda: - data submission updates - analysis group meeting in Geneva: practicalities, program - miRNA data processing - mRNA data processing: Micha will present his pipeline - batch effects and normalization The call details are below. best regards, Tuuli 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, 7 months

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