geuvadis_rna_analysis March 2012

geuvadis_rna_analysis@lists.crg.es

7 participants
9 discussions

by Natalja Kurbatova

Hi, Our systems group has done FTP accounts synchronization. The last step is smth called "the final merge". They have to disconnect both accounts in order to accomplish it. *Monday morning from 8AM till 11 AM our Geuvadis FTP sites will be not available. * After that time everything should work as normal: - the *same login details* as it was before - *both Aspera and FTP* connections are supported Regards, Natalja -- Natalja Kurbatova, PhD Functional Genomics Group, EBI

13 years, 1 month

[Geuvadis_rna_analysis] Geuvadis analysis group TC March 22 - Minutes

by Tuuli Lappalainen

Dear all, Here are the minutes of the Geuvadis RNAseq analysis group call of March 20. The next call will be in two weeks, April 5th. *Action items: *- Berlin should upload the miRNA sample information sheet to the ftp site asap - People should send Mathias from Uppsala the RNA quality info that he has asked for - Those who want to present on a specific topic at the analysis group meeting should email Tuuli - Everyone who wants to be involved in miRNA analysis should send Esther (esther.lizano(a)crg.es) an email Data submissions - All mRNA data is submitted. Tuuli will go through all the files, checksums and sample info for a final fastq freeze. - All the miRNA data has been submitted except for Kiel that had sequencer issues and Munich that postponed the run. We'll proceed with the analysis of the data that we have thus far (Tuuli will check these files and sample info as well), and add these missing ~100 samples later. - Mathias from Uppsala needs RNA quality data of the 5 replicate samples - please send it to him Analysis group meeting - Tuuli will put together a preliminary program. Those who want to present on a specific topic should send Tuuli an email, otherwise / in addition there will be 45-60min slots for all the labs to talk about analysis that they've done/planned. We'll brainstorm the first day and put together a practical analysis plan on the second day. miRNA processing - the Barcelona miRNA pipeline will be used to process (map, quantify) the miRNAs. They'll start downloading the data as soon as possible. Tuuli prepare the alternative allele miRNA reference sequences - People who want to be involved in the miRNA analysis should let Esther know mRNA processing - Micha presented their pipeline for mapping and quantification. The mapping statistics of Geuvadis samples look good, no huge lab effects. - the fact that GEM isn't published yet is a problem, and in Manolis's opinion we should use another mapper if the manuscript is not submitted by the end of April. Thus far we'll work with the GEM bams, but Tuuli will check with Natalja if EBI could map everything with bwa as a precaution. 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, 1 month

[Geuvadis_rna_analysis] Geuvadis analysis group TC March 22

by Tuuli Lappalainen

Hello, We'll have a Geuvadis analysis group call on Thursday (March 22) at 2pm. On the agenda: - data submission updates - analysis group meeting in Geneva: practicalities, program - miRNA data processing - mRNA data processing: Micha will present his pipeline - batch effects and normalization The call details are below. best regards, Tuuli Spain 902 125 136 Other countries +34 91 495 18 99 Participants' Pin-code: 764989* -- 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, 1 month

[Geuvadis_rna_analysis] FTP account

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

13 years, 1 month

[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

13 years, 1 month

[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

13 years, 1 month

[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

13 years, 1 month

[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

13 years, 1 month

[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

13 years, 1 month

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geuvadis_rna_analysis March 2012