geuvadis_rna_analysis

geuvadis_rna_analysis@lists.crg.es

160 discussions

[Geuvadis_rna_analysis] RNAseq TC on Feb 14th - main paper in revision

by Tuuli Lappalainen

Dear all, Good news from Nature - the main paper is back in the game, we'll be allowed to revise the paper! Let's have an analysis group TC on Thursday Feb 13th at 4pm CET to discuss the revisions. I'll send you a list of the revisions by tomorrow morning. best, Tuuli Call details: 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] 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

[Geuvadis_rna_analysis] draft RNA-seq qc

by P.A.C._t_Hoen＠lumc.nl

Dear all I attach the current draft of the RNA-seq QC paper, which was submitted as supplementary material for the main paper. We intend to submit the QC paper to Nat Biotechnology within the coming weeks. Please send your comments and edits (with track changes) to the current draft ulitmately December 21st Have a very good X-mas! Best wishes Peter Dr. Peter A.C. 't Hoen Center for Human and Clinical Genetics Leiden University Medical Center Postal zone S4-P PO Box 9600 2300 RC Leiden The Netherlands phone: +31-71-5269421 fax: +31-71-5268285 e-mail: p.a.c.hoen(a)lumc.nl

11 years, 10 months

[Geuvadis_rna_analysis] Analysis group TC November 29th

by Tuuli Lappalainen

Hello, We'll have a Geuvadis RNAseq analysis group TC on November 29th at 2pm CET. It will probably be a relatively short call. The agenda: - contents of the papers (main & companions) - timelines of the papers - LoF collaboration with the GTEx consortium - AOB Call details: Germany +49 692 573 804 41 <tel:%2B49%20692%20573%20804%2041> Netherlands +31 108 920 271 <tel:%2B31%20108%20920%20271> Spain +34 931 816 661 <tel:%2B34%20931%20816%20661> Sweden +46 840 309 949 <tel:%2B46%20840%20309%20949> Switzerland +41 58 262 07 22 <tel:%2B41%2058%20262%2007%2022> United Kingdom +44 203 370 57 19 <tel:%2B44%20203%20370%2057%2019> United States +1 646 381 08 89 <tel:%2B1%20646%20381%2008%2089> /Access code: 611683 / 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, 10 months

[Geuvadis_rna_analysis] main paper draft

by Tuuli Lappalainen

Hello all, Here is the draft of the Geuvadis main paper for the analysis group to read and comment. It's still a bit rough, but you get the idea. I'd like to ask you to send comments to me by *Saturday noon* - track changes in word, or write comments in an email. There are still some analysis items and material missing; see the updated action items below and please *complete your tasks**as soon as possible, by Saturday noon at the very latest. * The schedule is tight because we can't let our competitors get too far ahead of us. I'll aim to finish at least 99% of the numbers, results, and changes suggested by you by early next week, after which we circulate the paper with the whole group and submit in early December. There are 5 files: - main paper text (note that links to figures are not necessarily all up to date) - main figures and a table - supplementary methods (feel free to add text here) - supplementary figures (tables are not done yet) - legends for supplementary figures and tables (feel free to add text here) We're not there yet, but I can almost see the light at the end of the tunnel... best, Tuuli - Jean: look a bit into classification of sQTL changes - Gabrielle: figure out what will be the stable www address of the wiki - Matthias update splice junction calculations calculate how many splice junctions (out of total) have soft splicing in 1) any individual 2) all individuals. - Micha: Once/if we have the splice junction updates, analyze population frequency / annotation status distribution - Natalja: send supplementary methods text of imputation protocol send supplementary methods text of visualization continue working on visualization tracks - Peter/Irina: analyze repeat eQTL data - Thomas look at editQTLs - Jonas: replot read and gene count histograms - Manny: get numbers of LoF variants (total and covered by RNAseq data) estimate the number of stop+ that are truly NMD - Tuuli (FYI...a lot of work for me...) analyze causal variant discovery and GWAS causal variants run independent eQTL analysis run and plot annotation enrichments of sQTLs plot MDS for peer-corrected mRNA data polish text, legends and a few figures, integrate comments, text and plots from others, add references analyze rare variant mapping if any time remains (unlikely) -- 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, 11 months

[Geuvadis_rna_analysis] analysis group TC November 22

by Tuuli Lappalainen

Hello, Let's have an analysis group call today (22th) at 2pm CET. On the agenda: - action items for the main paper - main paper draft - companion papers Call details: Germany +49 692 573 804 41 <tel:%2B49%20692%20573%20804%2041> Netherlands +31 108 920 271 <tel:%2B31%20108%20920%20271> Spain +34 931 816 661 <tel:%2B34%20931%20816%20661> Sweden +46 840 309 949 <tel:%2B46%20840%20309%20949> Switzerland +41 58 262 07 22 <tel:%2B41%2058%20262%2007%2022> United Kingdom +44 203 370 57 19 <tel:%2B44%20203%20370%2057%2019> United States +1 646 381 08 89 <tel:%2B1%20646%20381%2008%2089> /Access code: 611683 / 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, 11 months

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