geuvadis_rna_analysis February 2012

geuvadis_rna_analysis@lists.crg.es

13 participants
16 discussions

by Natalja Kurbatova

Hi, QC results made by Mat Davis from EBI Anton Enright's is in attachment. The results are very similar to what Tuuli had. Guidelines and explanation of peaks around 35 bp are coming (Monday-Tuesday). Sorry for the delay and please let me know if you have any questions. Regards, Natalja -- Natalja Kurbatova, PhD Functional Genomics Group, EBI

12 years, 8 months

[Geuvadis_rna_analysis] Geuvadis RNAseq AG call on Thursday

by Tuuli Lappalainen

Hello all, We have the Geuvadis analysis group TC on Thursday (Feb 8) at 2pm. On the agenda: - updates on sequencing if needed - analysis group face-to-face meeting *Please fill the Doodle! http://www.doodle.com/24a4i3n8bkynhpwx *- small RNA QC - Manuel Rivas will present some slides on LOF analysis plans Here are the 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, 8 months

[Geuvadis_rna_analysis] Geuvadis RNAseq analysis group face-to-face meeting

by Tuuli Lappalainen

Dear all, The Geuvadis RNAseq analysis group is planning to have a face-to-face meeting in April. Please *fill in the Doodle by the end of the week* (Feb 12) if you think you would like to attend**so that we can fix the date of the meeting: *http://www.doodle.com/24a4i3n8bkynhpwx* The goal of the meeting is to present first results as well as plan and decide on future analyses. The 1.5-day meeting will probably take place in Geneva. 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, 8 months

[Geuvadis_rna_analysis] phiX

by P.A.C._t_Hoen＠lumc.nl

Dear all We are about to sequence the RNA-seq samples. We spike in phiX at 1% for QC reasons. Do people also still reserve one full lane for phiX to improve base calling? What have people done for their GEUVADIS RNA-seq samples? 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

12 years, 8 months

[Geuvadis_rna_analysis] Geuvadis seq data processing guidelines

by Tuuli Lappalainen

Hi all, Here are the guidelines for producing and submitting the fastq files. All this can be found from the wiki site, under Data Storage -> FTP (http://www.geuvadis.org/group/geuvadis/wikis/-/wiki/Main%20Geuvadis%20Wiki/…) If you don't have a password for the wiki, contact Gabrielle (gabrielle.bertier(a)crg.eu) best regards, Tuuli *FTP access* * The fastq files are to be uploaded to the Geuvadis private FTP account at EBI. Here are login details: o Host: ftp-private.ebi.ac.uk o User: geuvadis o Password: k2vP3kjJ o Directory: /upload/geuvadis/wp4_rnaseq/ o Contact Natalja Kurbatova (natalja at ebi.ac.uk) if you have technical problems. 1. Create fastq files * Use CASAVA 1.8, allow 1 mismatch in the index, demultiplex * Naming of fastq files: SAMPLE_ID.SeqLabNumber.M/MI_YYMMDD_Lane_Read.fastq.gz . SeqLabNumber has been given in the sample information sheets. M/MI stands for mRNA or miRNA sequencing. YYMMDD is the sequencing date. Example: NA12345.1.MI_111215_3_1.fastq.gz would be sample NA12345 miRNA-sequenced in Geneva on 2011-Dec-15 on lane 3. * Compress fastq files with either gzip or bzip2 2. Generate MD5 checksums for compressed fastq files files * The md5sum program is installed by default on most Unix, Linux and Unix like systems. o *Unix/Linux*: md5sum <file1> <file2> <etc> > myvalues.md5 o *Mac*: md5 <file1> <file2> <etc> > myvalues.md5 * This will create md5sum values for the files listed and save these values into a file called 'myvalues.md5' 3. Create a README file Link samples and uploaded files, and provide submitter info in a tab-separated file. An example attached. *4. Get sample information sheet * Find the filled sample information sheet that follows the template that was sent with the samples. If you're submitting only a part of your samples, please upload only that part of the file. E.g. "Geuvadis_samplesheet_mRNA_UNIGE_submission1.xlsx". *5. Upload * Upload the following files to ftp-private.ebi.ac.uk/upload/geuvadis/wp4_rnaseq/main_project/sequence_data/fastq/mrna or /mirna 1. Compressed fastq files 2. md5sum file 3. README file 4. sample information sheet * Data submission deadline* * The fastq submission deadline is February 15, 2011 * Please submit data when it's done - don't wait for the deadline. We don't want to transfer and map 2 x 500 files at the same time. * If there are unexpected delays in your data production, inform the other partners (especially Geneva) as soon as possible -- 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] Fwd: Geuvadis RNAseq AG call on Thursday

by Tuuli Lappalainen

Hello all, Here are the call details for today's TC: 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 -------- Original Message -------- Subject: Geuvadis RNAseq AG call on Thursday Date: Tue, 31 Jan 2012 18:53:51 +0100 From: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch> To: geuvadis_rna_analysis(a)lists.crg.es Hello all, We'll have out next Geuvadis analysis group TC on Thursday January 2 at 2pm. Lots of things on the agenda: - sequencing updates - analysis group face-to-face meeting: time, duration, location - abstract for the Biology of Genomes meeting at Cold Spring Harbor - Marc will present results of the DNA contamination analysis - miRNA data processing and QC - analysis plans (see below) As we discussed on the last call, I'd like to start putting together a plan of what we all eventually want to do with the data. The data is of course shared and everyone is free to do what they want, but we need to make sure that the essentials get done and that there's no unnecessary overlap. As a starting point for discussion, take a look at the analysis breakdown draft that I wrote (https://docs.google.com/document/d/1_LAkv0NGSrXU6LSsyhN_GnZB4WRanl-e993U_0I…), and feel free to edit it before/during the call. 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, 8 months

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geuvadis_rna_analysis February 2012