[Geuvadis_rna_analysis] Geuvadis analysis group TC March 22 - Minutes

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