geuvadis_rna_analysis

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160 discussions

[Geuvadis_rna_analysis] Fwd: Geuvadis RNAseq AG call on Thursday

by Tuuli Lappalainen

Hello all, Here are the call details for today's TC: Spain 902 125 136 Other countries +34 91 495 18 99 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 -------- Original Message -------- Subject: Geuvadis RNAseq AG call on Thursday Date: Tue, 31 Jan 2012 18:53:51 +0100 From: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch> To: geuvadis_rna_analysis(a)lists.crg.es Hello all, We'll have out next Geuvadis analysis group TC on Thursday January 2 at 2pm. Lots of things on the agenda: - sequencing updates - analysis group face-to-face meeting: time, duration, location - abstract for the Biology of Genomes meeting at Cold Spring Harbor - Marc will present results of the DNA contamination analysis - miRNA data processing and QC - analysis plans (see below) As we discussed on the last call, I'd like to start putting together a plan of what we all eventually want to do with the data. The data is of course shared and everyone is free to do what they want, but we need to make sure that the essentials get done and that there's no unnecessary overlap. As a starting point for discussion, take a look at the analysis breakdown draft that I wrote (https://docs.google.com/document/d/1_LAkv0NGSrXU6LSsyhN_GnZB4WRanl-e993U_0I…), and feel free to edit it before/during 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

13 years, 3 months

[Geuvadis_rna_analysis] Geuvadis RNAseq AG call on Thursday

by Tuuli Lappalainen

Hello all, We'll have out next Geuvadis analysis group TC on Thursday January 2 at 2pm. Lots of things on the agenda: - sequencing updates - analysis group face-to-face meeting: time, duration, location - abstract for the Biology of Genomes meeting at Cold Spring Harbor - Marc will present results of the DNA contamination analysis - miRNA data processing and QC - analysis plans (see below) As we discussed on the last call, I'd like to start putting together a plan of what we all eventually want to do with the data. The data is of course shared and everyone is free to do what they want, but we need to make sure that the essentials get done and that there's no unnecessary overlap. As a starting point for discussion, take a look at the analysis breakdown draft that I wrote (https://docs.google.com/document/d/1_LAkv0NGSrXU6LSsyhN_GnZB4WRanl-e993U_0I…), and feel free to edit it before/during 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

13 years, 3 months

[Geuvadis_rna_analysis] Geuvadis analysis group TC minutes

by Tuuli Lappalainen

Dear all, Here are minutes of the Geuvadis analysis group TC on January 12. The next call has to be pushed forward by one week to *February 2 at 2pm. *We'll continue with the normal schedule after that, so the one after that will be February 9. best regards, Tuuli Action items: - Tuuli: Set up a call for next week to discuss imputation details with Natalja, Micha, Tim. Continue masked mapping tests - Esther, Peter, Natalja: Send an outline of you miRNA analysis pipeline to the analysis group mailing list - Everyone: Think and discuss in your lab about the analyses that you'd want to do (lead and/or participate) with this dataset, by the next call - Micha: Continue mapping tests - *Attending:* Tuuli, Micha, Esther, Ivo, Tim, Thomas x2, Mathias, Peter, Olof, Matthias, Natalja - *Sequencing:* Most of the labs will be able to meet the initial deadline of Feb 15 despite the delays in kit delivery, which is great. We agreed to keep the very last deadline of March 15; all the samples and reruns should be done and data submitted by then. - *Genotypes*: We need to impute about 40 samples that are not in 1000g Phase 1 (they have Omni 2.5M haplotypes). Natalia/EBI could probably do this, and Tuuli, Micha and Tim & co. want to be involved/informed too. This should be done within a month. - *miRNA analysis pipeline*: The labs who have experience of miRNA analysis will send around details of how they map and quantify miRNAs. We'll discuss on the next call how we should analyze them. - *A new collaboration:* Mark McMarthy from Oxford is a long-term collaborator of Manolis. They've developed a new kind of a burden test to look at rare variant effects, and expressed interest in doing some analysis with the Geuvadis data. People were positive about this, and Mark's postdoc Manuel Rivas will present their plans in a future TC. - *Analysis plans*: Tuuli would like to coordinate the future analyses so that the essentials get done and there's no unnecessary overlaps. For this we also need to assign people who will lead/participate/be informed for each set of analysis. In the next call we'll start putting together a list of what will be done and by whom. - *Analysis group face-to-face meeting*: It would be good to get together to discuss in real life once the data is ready and gone through basic pipelines - maybe around April. - *mRNA mapping*: The GEM paper will be submitted soon, so we might want to use Micha's pipeline for mapping, quantification and normalization as the basic approach. Micha presented some slides about an approach that they're developing for SNP calling from RNAseq data, based on excessive mapping. Tuuli presented results suggesting that reference allele mapping bias affects exon quantifications. We should correct for it e.g. by mapping to a masked reference. -- 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

13 years, 3 months

[Geuvadis_rna_analysis] GEUVADIS RNAseq TC

by Gabrielle Anne Bertier

Dear all, at the request of Tuuli, please fill in this doodle<http://www.doodle.com/ccm7dkvtngwwquqt> for the next GEUVADIS RNAseq TC. Preliminary agenda: - update on sequencing progress - preliminary QC/analysis results - analysis plans - analysis group meeting in the spring Kind regards, Gabrielle http://www.doodle.com/ccm7dkvtngwwquqt

13 years, 3 months

[Geuvadis_rna_analysis] Geuvadis TC - slides

by Tuuli Lappalainen

Hi all, Here are some slides about reference allele bias corrections in mapping for the Geuvadis analysis group TC that will be in 10 minutes. 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

13 years, 3 months

[Geuvadis_rna_analysis] Geuvadis RNAseq analysis group TC on Thursday

by Tuuli Lappalainen

Dear all, We'll have the Geuvadis RNAseq analysis group call this Thursday, January 12, at 14-15pm. I hope many of you can attend. We should discuss at least the following things: - updates on sequencing progress and deadlines - genotypes and imputation - mRNA mapping and quantification approaches (Tuuli will present a few slides) - miRNA analysis pipeline - possible collaboration with Mark McCarthy's group Call details: Spain 902 125 136 Other countries +34 91 495 18 99 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

13 years, 3 months

[Geuvadis_rna_analysis] Geuvadis mRNA data from unige

by Tuuli Lappalainen

Hello and happy new year! The first batch of Geuvadis mRNAseq data from UNIGE is now available at the ftp site. If you're interested in taking a look at these 103 samples, feel free to do so. The fastq files and the sample info can be found from /upload/geuvadis/wp4_rnaseq/main_project/sequence_data/fastq/mrna Of these data, I've defined sandbox datasets for testing purposes as we discussed - see the Analysis page of the wiki. There's a small set of 5 samples that I chose to be those that we're doing in replicate in all the labs. For a little big bigger scale testing, I fixed a set of 24 samples (the 5+19 others). Of these 24, I have uploaded the bam files from mapping with bwa in: /upload/geuvadis/wp4_rnaseq/main_project/working/mapping/bam/normal_hg19/bwa . As agreed before, we'll have an *analysis group TC next week, January 12, at 2pm*. I'll send the agenda (and a reminder) next week. 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

13 years, 4 months

[Geuvadis_rna_analysis] Geuvadis RNAseq analysis group TC minutes

by Tuuli Lappalainen

Hello all, A brief summary of the first analysis group TC. Action items in *bold*. Next call Thursday January 12, 2pm. Attending: Tuuli, Micha, Natalja, Marc, Mathias, Tim, Olof, Marta 1) Kit situation - Geneva and Barcelona have both mRNA and miRNA kits - Berlin and Kiel have miRNA kits - Munich, Uppsala and Leiden (?) don't have any kits - *All the labs* should send Tuuli an update before Christmas indicating if they have received the kits or not. We'll wait until early January and see then if we need a plan B. - the labs that have kits are on schedule with the sequencing 2) Low-level data processing (mapping, quantification etc.) - *Tuuli* will upload the fastq files and bams (from bwa) from their mRNA seq by the end of the week. * - Tuuli* will define a sandbox dataset of 24 and 5 samples from UNIGE for testing purposes. - *Micha* will find out when GEM is likely to be published - We shouldn't spend too much time figuring out how to map the reads - this has been done already. However, there are a couple of things that we should test: - *Marc* will analyze the level of genomic contamination in the 24 samples - Tuuli has concerns about reference allele mapping bias affecting quantifications. *Natalja* will run Tophat for 5 samples with the normal reference (hg19) and a reference masked for all common 1000g variants (Tuuli will provide this) to see if masking leads to a big loss in mapping. *Micha *will check whether it's possible with GEM. If masking is not feasible, we can consider other options for dealing with this bias... The following was planned for the final dataset: - Micha will run his whole pipeline (GEM for mapping, SNAPE for variant calling, Flux for deconvolution and normalization, AStalavista for alternative splicing analyzes..). - Natalja will run the EBI pipeline using bwa and/or tophat, and quantify exon counts and/or RPKMs. bwa+exon counts would enable direct comparison with earlier eQTL results from Manolis's lab - regarding normalization, both PCA and specific covariate based approaches are possible - we'll have to see what the data looks like - all analyses should be run with duplicates - Geneva has seen that in RNAseq data duplicates rarely seem to be PCR artefacts 3) FTP instructions - *Natalja* will send an email to the analysis group about the FTP instructions that are now on the ftp site I hope I remembered at least the most important things! I'll let you know when the data is one the ftp site. 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

13 years, 4 months

[Geuvadis_rna_analysis] Geuvadis RNAseq analysis group TC

by Tuuli Lappalainen

Hi all, Thanks for the quick replies to the doodle about the Geuvadis analysis group TCs. It seems that *Thursday 2pm CET* is the best time, so please keep that slot free for next spring. Let's have calls every 2 weeks by default, starting on January 12. But we should have one call before Christmas and start with an exception since next week's Thursday is impossible for me. So let's have a TC on *Tuesday December 13th at 3pm*. As I said before, those who want to do mapping etc. to the raw data should send an email with a brief description of their pipeline before the call. cheers, Tuuli PS. Marta, I'm sorry that I had to pick a time that wasn't good for you - the other times would have had even more people missing. I hope you can join at least sometimes or find someone else who could attend the call instead. -- 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

13 years, 4 months

[Geuvadis_rna_analysis] RNAseq Analysis Regular TCs

by Gabrielle Anne Bertier

Dear all, As suggested by Tuuli, we will set up a regular time for the Geuvadis RNAseq analysis group TCs, and try to have the first call before Christmas. Please fill in the doodle<http://www.doodle.com/bc2ewnuc4rtsu4u6> and mark whether the suggested times of the week are good for you in general (even if you can't participate on this particular week). Full doodle link: http://www.doodle.com/bc2ewnuc4rtsu4u6 On the agenda: - progress of sequencing, the kit issue - further specifications on sequencing protocols if needed - low-level analysis pipeline(s) to use: anyone who wants to do mapping-quantification-normalization of this dataset should send a brief summary of their methods to geuvadis_rna_analysis(a)lists.crg.es<mailto:geuvadis_rna_analysis@lists.crg.es?subject=Mapping-quantification-normalization%20method%20summary> before the call. So far are on the RNA_analysis list: (if you want to be added do the list please just send me an email) esther.lizano(a)crg.es gmicha(a)gmail.com mgut(a)pcb.ub.es olof.karlberg(a)medsci.uu.se P.A.C._t_Hoen(a)lumc.nl p.rosenstiel(a)mucosa.de roderic.guigo(a)crg.cat rodericguigo(a)gmail.com sultan(a)molgen.mpg.de Tuuli.Lappalainen(a)unige.ch Kind regards, Tuuli & Gabrielle

13 years, 5 months

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