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