FTP access

• The fastq files are to be uploaded to the Geuvadis private FTP account at EBI. Here are login details:
  • Host: ftp-private.ebi.ac.uk
  • User: geuvadis
  • Password: k2vP3kjJ
• Directory: /upload/geuvadis/wp4_rnaseq/
• 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.
  
  • Unix/Linux: md5sum <file1> <file2> <etc> > myvalues.md5
  • 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