Hello all, Here are the minutes of the Geuvadis analysis group TC of March 8. The next call will be on March 22. *Action items*: - everyone should upload any missing fastqs that they have ready, and whatever is not should be produced asap - Thasso will upload the mRNA bams from GEM that are ready, and continue mapping the rest of the mRNA data - Tuuli will analyze EB virus expression in further detail - Marc F will see if the Barcelona miRNA pipeline can cope with our ~450 samples - Tuuli will look into producing alternative allele precursor miRNA reference sequences for mapping those loci that overlap a genetic variant - Natalja and Tuuli will finish the genotype file - Analysis group meeting in Geneva: Tuuli has sent an email about the registration. The form is in https://docs.google.com/spreadsheet/viewform?formkey=dE1vZEV3ZmlubFBZUkxHMk… , deadline March 16. - most of the sequencing data has been uploaded on the ftp site - a few mRNAs are missing and about 100 miRNAs. - imputation is done, and our official, final genotype file should be ready next week - mRNA analysis: - Thasso from Barcelona has mapped about 350 samples with GEM thus far, the rest is running. He'll start uploading the bams to the ftp site - Tuuli has mapped the 24 sandbox samples including the Epstein-Barr virus in the reference (the virus is used in the LCL transformation). The virus seems to have quite high and variable expression levels in many of the samples (RPKM 5-60, median 17). Tuuli will do more analysis to see if we need to include this as a covariate in the analyses. - miRNA analysis - Henk from Leiden presented some results of Leiden's miRNA samples. About 20% of the reads seem to be from miRNAs, which is not bad given the quality of the data from the other labs. He also noted that other small RNA types are also well represented, especially snoRNAs - we should definitely analyze these as well and not just focus on the miRNAs - Marc from Barcelona presented a summary of the Barcelona miRNA pipeline that can do QC, quantification, novel miRNA and isomir detection. Marc will test if the pipeline can cope with all of our samples; alternatively e.g. the Leiden pipeline could be used. Tuuli will look into producing alternative allele precursor miRNA reference sequences for mapping those loci that overlap a genetic variant. 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_rna_analysis] Geuvadis RNAseq analysis group TC on March 8 Date: Wed, 07 Mar 2012 13:52:19 +0100 From: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch> To: geuvadis_rna_analysis(a)lists.crg.es Hello all, We'll have our biweekly Geuvadis RNAseq analysis group call on Thursday at 2pm. Things to discuss: - sequencing and data submission progress - mRNA analysis and mapping progress - miRNA analysis - Henk will present some stats of the sequencing in Leiden - Marc F will present the Barcelona miRNA analysis pipeline The call details are: 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