geuvadis_rna_analysis December 2011

geuvadis_rna_analysis@lists.crg.es

5 participants
3 discussions

[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, 4 months

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geuvadis_rna_analysis December 2011