Dear all,
I have uploaded the raw fastq files for the 5 common samples. I have
included md5sum info in README_mirna_common_samples_cnag.txt file.
Best wishes,
Sergi
---------------------------------
Sergi Beltran Agulló
Bioinformatics Analysis Group
CNAG - National Center for Genomic Analysis
Parc Científic Barcelona - Torre I
Baldiri i Reixac 4, 2a p.
08028 Barcelona
(+34)934033748
sbeltrana(a)pcb.ub.cat
---------------------------------
On 02/21/2012 04:21 PM, Tuuli Lappalainen wrote:
Hello all,
We had a short TC on miRNA QC, and decided to do QC analysis also on
the 5 replicate samples. *All the labs that have miRNAseq data, please
upload the replicate miRNA fastq files into the ftp site* (HG00355,
NA06986, NA19095, NA20527, HG00117). See below for ftp and file naming
details.
To summarize what we've learned thus far, the quality of the data is
not great in any of the labs, but it's not hideously bad either. Kiel
and Geneva will sequence deeper to get more coverage, whereas the data
from Barcelona and Berlin seems to be as good as it gets with these
RNAs and this method. Many thanks to Matthias from Kiel and all the
people (Esther/Sergi/Marc...) in Barcelona for doing the QC analyses.
I hope the remaining 3 labs will have data soon to assess the quality.
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
On 2/15/12 11:14 AM, Tuuli Lappalainen wrote:
> Hello,
>
> So, I'd like to ask all the labs that have miRNA data to upload 3
> fastq files to the ftp site.
>
> I just uploaded our files, and I'll be expecting files from Barcelona
> (Marta/Esther/Sergi), Berlin (Marc), Kiel (Matthias). Does Munich
> have miRNA data? Please do this asap.
>
> Detailed instructions:
> - upload to
> ftp-private.ebi.ac.uk/upload/geuvadis/wp4_rnaseq/main_project/working/miRNA_QC
> . User geuvadis, password k2vP3kjJ .
> - to make the file processing easy, please name the fastq files
> according to the naming instructions:
> SAMPLE_ID.SeqLabNumber.MI_YYMMDD_Lane_1.fastq.gz . The lab numbers
> are: Geneva=1, Barcelona=2, Berlin=3, Kiel=4, Munich=5. E.g. one of
> our files is HG00096.1.MI_120104_4_1.fastq.gz
> - choose 3 random files, or pick ones that have a little bit
> different numbers of total reads
> - upload also a readme file with at least your name and email and the
> read length
> - use raw fastq files without any adaptor trimming, or if you want,
> you can trim all the reads to 36 bp
>
> thanks,
> 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
>
>
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