2 Feb
2012
2 Feb
'12
6:49 p.m.
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