geuvadis_rna_analysis January 2013

geuvadis_rna_analysis@lists.crg.es

4 participants
5 discussions

[Geuvadis_rna_analysis] RNAseq TC on Thursday 31st at 4pm CET

by Tuuli Lappalainen

Hello, We'll have an RNAseq analysis group TC on Thursday the 31st at 4pm CET. On the agenda: - upcoming conferences - our future projects using Geuvadis data - main paper updates (no major news yet) - companion paper updates - web page / wiki If you can't attend the call but you're thinking of submitting a Geuvadis-related abstract to a conference, or if you're working on a project that uses Geuvadis data, please send me an email (before the call = now) so that we'll know. best, Tuuli The numbers are: SPAIN 900800678 GERMANY 08001013982 NETHERLANDS 08002658044 FRANCE 0800947739 UNITED KINGDOM 08005285280 UNITED STATES 8005369053 SWEDEN 0201400578 >From Other countries +34 917911859 Access code: 3160100 -- Tuuli Lappalainen, PhD Department of Genetics, Stanford University School of Medicine , and Department of Genetic Medicine and Development, University of Geneva Email: tuuli.e.lappalainen(a)gmail.com / tlappala(a)stanford.edu Tel: +1 415 351 9713 Bustamante lab Department of Genetics 300 Pasteur Dr. Lane L301 Stanford, CA 94305-5120 USA

11 years, 8 months

[Geuvadis_rna_analysis] data files for future release

by Tuuli Lappalainen

Hello, I've organized the quantification and QTL files that I suggest that we release when the paper is eventually published (no news from Nature yet). The attached exel sheet contains brief descriptions and FTP locations of the data files as well as sample information files (note that it has multiple sheets). I'll prepare more detailed documentation before the files go public. In summary, I suggest that we release the following files. Any objections / additions? - quantifications of exons, transcripts, genes, repeats, miRNAs, RNA edited sites. Of all these: raw counts and library depth corrected quantifications of all QC-passed samples, as well as PEER-normalized files of nonredundant samples. - QTLs of all the above: all significant associations and best association per gene for both CEU and YRI. Natalja, you can start organizing the files, but do NOT release them to the public yet. best, Tuuli -- Tuuli Lappalainen, PhD Department of Genetics, Stanford University School of Medicine , and Department of Genetic Medicine and Development, University of Geneva Email: tuuli.e.lappalainen(a)gmail.com / tlappala(a)stanford.edu Tel: +1 415 351 9713 Bustamante lab Department of Genetics 300 Pasteur Dr. Lane L301 Stanford, CA 94305-5120 USA

11 years, 8 months

[Geuvadis_rna_analysis] RNAseq paper

by Tuuli Lappalainen

Dear all, The Geuvadis RNAseq paper was rejected this morning. We've decided with Manolis that we should make an appeal, and we have already been in touch with Magdalena about this. We'll need to send her a response letter in a couple of days (see the attachment with reviewer's comments and a rough response draft). It ain't over til it's over. Since we were going to have a call soon anyway, let's have a *TC on Thursday the 24th at 4pm CET*. Before that, I'd be happy to hear your *comments to the response letter (deadline: immediately)*. There's a couple of bigger items to discuss, and specific questions to a few of you - see below. There won't be a lot of new analysis to do if we're given the chance to revise. Questions: - Do we drop non-essential analyses as #2 suggests? This would mean RNA editing, maybe fusions and subtle splicing. I'm not keen to, but if people think it would improve the overall quality of the paper... - Should we restructure the supplement by topic instead of methods/figures/tables? Need to ask Magdalena too. - Andrew & Natalja: Can we add a data slicing and download function to the browser (or a separate site linked from the browser)? - Jean & Mar: How is the qualitative/quantitative analysis affected by low-abundance transcripts? Will the results change if the threshold is different? - Jean, Mar, Pedro, Micha (and myself): #2 raises an important question (really!): most of transcript variation is explained by transcript ratio differences, but we find very few QTLs for this. Why do you think this is? Is all that variation really just random/environmental/epigenetic? - Jean: #3 suspects that the 3% of transcriptome variation explained by population could be just random - how do we respond to this? - Manny: What could we do to add novelty value to NMD analysis? - Gabrielle: Is it possible to make a read-only password for the wiki? We could give one to the reviewers just so that they can see it. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetics, Stanford University School of Medicine , and Department of Genetic Medicine and Development, University of Geneva Email: tuuli.e.lappalainen(a)gmail.com / tlappala(a)stanford.edu Tel: +1 415 351 9713 Bustamante lab Department of Genetics 300 Pasteur Dr. Lane L301 Stanford, CA 94305-5120 USA

11 years, 8 months

[Geuvadis_rna_analysis] RNAseq TC

by Tuuli Lappalainen

Hello all, *Please fill in a Doodle by Friday *for a new Geuvadis RNAseq call time: http://www.doodle.com/hrgvdn5drnd845sh . No news from the paper... But it would be good to have a call to catch up on a couple of things: - upcoming conferences and presentations (ESHG, The Next NGS Challenge Conference, Biology of Genomes) - future companion/spin-off projects using Geuvadis data - other updates I'm now in California, so our old 2pm CET slot would be just too early for me. The Doodle is for a new time that we can use when needed, not in a weekly basis. The poll has time zone support on the upper left side. best, Tuuli -- Tuuli Lappalainen, PhD Department of Genetics, Stanford University School of Medicine , and Department of Genetic Medicine and Development, University of Geneva Email: tuuli.e.lappalainen(a)gmail.com / tlappala(a)stanford.edu Tel: +1 415 351 9713 Bustamante lab Department of Genetics 300 Pasteur Dr. Lane L301 Stanford, CA 94305-5120 USA

11 years, 9 months

[Geuvadis_rna_analysis] headache

by Tuuli Lappalainen

Hello, Happy new year to all of you, I hope you've enjoyed your holidays. The good news that I have to tell is that the RNAseq paper is under review; Magdalena told me this just before Christmas. So we can expect news from there in a couple of weeks. The bad news is that as I was going through some data files, I discovered a bug that is non-fatal but still needs to be fixed - and it's very early on in the process. In the processing of quantifications when I correct for the total number of mapped reads (the 45N in the file names), I've made an indexing error and corrected for the total number of unmapped reads instead. These two are very highly correlated, (see attachment; only the correlation and not the absolute numbers matter), so I'm 98% sure that none of the biological results will change. I already reran the repeat eQTL analysis for Europeans: Previously we had 5652 repeats with an eQTL, and after correction of the bug there's 5588, of which 5239 are the same as before - the difference in total numbers is 1%, and we both lose and gain some, with a total 7% change. I think this is not too bad, and I expect similar results from other reruns that I'm working on now. Permutation results were identical so I won't need to rerun them. The bug affects non-RPKM-based quantifications (exons, repeats, and LoF analyses of junctions, introns), eQTL analyses of exons and repeats, miRNA-mRNA correlations, QC analyses based on exon quantifications. Transcript and gene level analyses are based on RPKMs and are unaffected, as are miRNA quantifications. Needless to say, I'm extremely sorry and very angry at myself that I screwed up in such an early step. Most but not all of the analyses that need to be reran are mine, and deep apologies for the extra work that this will cause. If there is any analysis where you have used files with 45N, it needs to be updated. I will be rerunning things - starting from the files that affect others - during the next couple of days and will be in touch with the relevant people individually. FYI, I'm moving to San Francisco on the 8th, so being on the Pacific time zone will affect my email reaction speed and schedules of any conference calls. best, 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

11 years, 9 months

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geuvadis_rna_analysis January 2013