geuvadis_rna_analysis

geuvadis_rna_analysis@lists.crg.es

160 discussions

by Natalja Kurbatova

Hello, Update on FTP account: The synchronization of old and new one FTP accounts will take quite a while. Meanwhile, we can use old account "geuvadis" for small transfers (uploads and downloads). NB! Aspera server is not available for it anymore. I will confirm you when the synchronization process is complete and Aspera is back in action. Regards, Natalja -- Natalja Kurbatova, PhD Functional Genomics Group, EBI

12 years, 7 months

[Geuvadis_rna_analysis] IMPORTANT!!! FTP account

by Natalja Kurbatova

Hello, We have problems with FTP account (too many connections and as the result server time out message). EBI systems group created a new account for the Geuvadis (high performance account). Now we have to merge two accounts together. *Could you please stop all the transactions on FTP site for few hours starting from now?* I will send an e-mail around as soon as we are ready (one-two hours). Regards, Natalja -- Natalja Kurbatova, PhD Functional Genomics Group, EBI

12 years, 7 months

[Geuvadis_rna_analysis] Geuvadis RNAseq analysis group TC on March 8

by Tuuli Lappalainen

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

12 years, 7 months

[Geuvadis_rna_analysis] Geuvadis RNAseq analysis group meeting

by Tuuli Lappalainen

Dear all, We will have a face-to-face meeting for the Geuvadis RNAseq analysis group in Geneva on April 16-17. The goal of the meeting is to present first results and plan future analyses. Everyone involved in the project is welcome to attend, and we hope that especially those who plan to contribute to data analysis will be able to come. *If you would like to attend the meeting, please fill out the following registration form by March 16*: https://docs.google.com/spreadsheet/viewform?formkey=dE1vZEV3ZmlubFBZUkxHMk… The preliminary schedule can be found in: https://docs.google.com/document/d/1xzm154L2ZD8qEgl9E4cKsoeuAhCLJZ4c6ZXiM3U… Practicalities: - Everyone should book their own flights - We will arrange and pay lunch and coffee on the 16th and 17th, and a dinner on the 16th - For accommodation, we can recommend two hotels listed below. If you want to stay in either of them, you can make your own reservation or we can do it for you - just fill in the relevant information in the registration form. You can also stay elsewhere and arrange it yourself. 1. Hotel du Midi ~190 CHF + breakfast = ~ 220 CHF Place Chevelu 4, 1201 Geneva - phone +41 22 544 15 00 webpage: http://www.hotel-du-midi.ch/ 2**. Hotel "Bel'Espérance" single CHF 125, double CHF 150, breakfast included Rue de la Vallée 1, 1204 Geneva phone +41 22 818 37 37 webpage: http://www.hotel-bel-esperance.ch/ Don't hesitate to ask me or our admin assistant Ancilla Stefani (Ancilla.Stefani(a)unige.ch) if you have any questions. 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

12 years, 7 months

[Geuvadis_rna_analysis] geuvadis file uploads and naming

by Tuuli Lappalainen

Dear all, Could I please ask everyone to submit the data that are ready? The few dropouts can be submitted later, and we still have a few weeks until the deadline, but it would be great to get the big data batches into the mapping pipelines as soon as they're done. For mRNA, we're lacking data from Kiel and Berlin, and for miRNA I am the only one who has submitted the data. A couple of file naming practicalities for special cases: - if you're running the same library on several lanes of the same run: please use just the first of the two lanes in the file name, but include both in the sample information sheet (e.g 3_4). - for miRNA, some labs (us and Kiel at least) had to rerun the same libraries twice to get more coverage. In such a case, please check that the quantifications are consistent for all the samples before merging the fastq files. In the file naming, use the date and lane of one of runs and include both in the sample information sheet column. 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

12 years, 7 months

[Geuvadis_rna_analysis] Geuvadis RNAseq analysis group TC

by Tuuli Lappalainen

Dear all, We'll have our Geuvadis RNAseq analysis group call again today (Thursday) at 2pm. Things to be discussed: - update on sequencing progress - miRNA QC issues - Tuuli will present some slides on how genetic variants affect mapability, and ways to correct for it - mRNA and miRNA data processing pipelines Call details: 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

12 years, 7 months

[Geuvadis_rna_analysis] Geuvadis RNAseq lab IDs

by Tuuli Lappalainen

Hello, We've found a slight discrepancy in the Geuvadis RNAseq lab ID number info. This is due to my mistake: In the RNAseq protocol text in November there's a table of lab IDs, but then I forgot about this and assigned partly different IDs when sending out the sample information sheets. This caused some confusion now that we've actually had data to exchange. Sorry about this, but I'm glad we caught it early (thanks Peter, Matthias, Olof). From now on, please use the following IDs that correspond to the sample information sheets. I also enclosed the sequencing protocol with an updated table. Because of this error, in the miRNAseq QC slides from Matthias the samples labeled as Leiden are actually from Uppsala. have a nice weekend, Tuuli Correct Lab # # in the previous protocol table UNIGE (Geneva) 1 1 CRG (Barcelona) 2 2 MPIMG (Berlin) 3 3 ICMB (Kiel) 4 4 HMGU (Munich) 5 7 UU (Uppsala) 6 5 LUMC (Leiden) 7 6 -- 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

12 years, 7 months

[Geuvadis_rna_analysis] Fwd: Fwd: Re: Geuvadis RNAseq analysis group TC - slides

by Tuuli Lappalainen

Hello, Here are miRNA QC results of the replicate samples from Matthias. 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: Fwd: Re: [Geuvadis_rna_analysis] Geuvadis RNAseq analysis group TC - slides Date: Thu, 23 Feb 2012 16:28:23 +0100 From: Matthias Barann <m.barann(a)ikmb.uni-kiel.de> To: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch> Hello Tuuli, could you please try to forward the attached pdf file to the others. I tried it in three different ways (as excel sheet, zip file and pdf) but always get an error. Thanks, Matthias -------- Original Message -------- Subject: Re: [Geuvadis_rna_analysis] Geuvadis RNAseq analysis group TC - slides Date: Thu, 23 Feb 2012 16:26:39 +0100 From: Matthias Barann <m.barann(a)ikmb.uni-kiel.de> To: geuvadis_rna_analysis(a)lists.crg.es Dear all, here is the quality analysis we have done on the common miRNA samples. There's one sample which shows a weird read-length for the genome mapping (NA20527, page 11-12). However, in the miRNA mapping it's not that much different anymore, but it misses some more miRNAs (page 6). And there are a few samples which show almost equal amounts of short reads (14 bp) compared to the number of 22 bp reads. Everything else looks quite similar. One other thing I noticed is, that the sample NA19095 seems to contain a (very little) bit more poly-A tagged RNAs (page 2, upper graph). This is probably due to the extraction, as all institutes have roughly the same amount of polyA-trimmed reads for the same samples. For mapping only reads were used, which had the adapter successfully removed. best wishes, Matthias -- Matthias Barann Institute of Clinical Molecular Biology Christian Albrechts University Kiel Schittenhelmstr. 12 D-24105 Kiel, Germany m.barann(a)ikmb.uni-kiel.de +49 - (0)431 - 597 8681 (office)

12 years, 7 months

[Geuvadis_rna_analysis] Geuvadis RNAseq abstract for Biology of Genomes

by Tuuli Lappalainen

Dear all, Here is the Geuvadis RNAseq draft for the abstract for the Biology of Genomes meeting. Please *comment and give your author and affiliation info by Tuesday Feb 21*. Regarding the author list: The length limitation includes author & affiliation info, so we need to keep it very short for this abstract. We suggest the following: - analysis people with major contribution: Tuuli Lappalainen, Michael Sammeth, Natalja Kurbatova, Tim Strom, Peter t' Hoen, Matthias Barann, Marc Sultan, Esther Lizano, Manuel Rivas. If someone else feels that they should be included, we can try to squeeze in an additional name or two. - One PI per institute - *Kiel and Berlin, please indicate who*: Alvis Brazma, Ann-Christine Syvanen, Thomas Meitinger, Gert-Jan van Ommen, Philip Rosenstiel */* Stefan Schreiber, Ralf Sudbrak */* Hans Lehrach, Ivo Gut, Xavier Estivill, Emmanouil T Dermitzakis - and last: "on behalf of the Geuvadis Consortium" *Everyone on the author list: please reply to this email with your name and affiliation info. *Due to length limitations, please include only your Geuvadis partner affiliation and use abbreviations when possible. best regards, Tuuli Author information example: First name: Tuuli Middle initial: Last name: Lappalainen Email: tuuli.lappalainen(a)unige.ch Affiliation name: University of Geneva Department: Dept of Genetic Medicine and Development Street: R. Michel Servet 1 City : Geneva Postal code: 1211 4 Country: Switzerland -- 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

12 years, 8 months

[Geuvadis_rna_analysis] miRNA test file upload

by Tuuli Lappalainen

Hello, So, I'd like to ask all the labs that have miRNA data to upload 3 fastq files to the ftp site. I just uploaded our files, and I'll be expecting files from Barcelona (Marta/Esther/Sergi), Berlin (Marc), Kiel (Matthias). Does Munich have miRNA data? Please do this asap. Detailed instructions: - upload to ftp-private.ebi.ac.uk/upload/geuvadis/wp4_rnaseq/main_project/working/miRNA_QC . User geuvadis, password k2vP3kjJ . - to make the file processing easy, please name the fastq files according to the naming instructions: SAMPLE_ID.SeqLabNumber.MI_YYMMDD_Lane_1.fastq.gz . The lab numbers are: Geneva=1, Barcelona=2, Berlin=3, Kiel=4, Munich=5. E.g. one of our files is HG00096.1.MI_120104_4_1.fastq.gz - choose 3 random files, or pick ones that have a little bit different numbers of total reads - upload also a readme file with at least your name and email and the read length - use raw fastq files without any adaptor trimming, or if you want, you can trim all the reads to 36 bp thanks, 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

12 years, 8 months

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

geuvadis_rna_analysis