Re: [Geuvadis_rna_analysis] Geuvadis analysis group TC minutes

Dear all Our miRNA pipeline was published in 2010 and is attached. One of the main features which it does differently from the competitors is that it does properly annotate the mature and star sequences of a miRNA and we have seen that they can behave very differently so it is a shame to just summarize those. Moreover, it produces some nice output with counts for each miRNA and other annotated small RNAs in a file that you can just open in Excel On another note: Irina, my PhD student, also joined the call Best wishes Peter ------------------------------------------------------------------------ *From:*geuvadis_rna_analysis-bounces@lists.crg.es [mailto:geuvadis_rna_analysis-bounces@lists.crg.es] *On Behalf Of *Tuuli Lappalainen *Sent:* Thursday, January 12, 2012 4:31 PM *To:* geuvadis_rna_analysis(a)lists.crg.es *Subject:* [Geuvadis_rna_analysis] Geuvadis analysis group TC minutes 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 ofGeneva Medical School CMU / Rue Michel-Servet 1 1211Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch <mailto:tuuli.lappalainen@unige.ch> _______________________________________________ Geuvadis_rna_analysis mailing list Geuvadis_rna_analysis(a)lists.crg.es http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis