Dear all,
I've uploaded three of the five common samples, as we don't have
sequencing data for the remaining two samples yet.
best wishes,
Matthias
On 21.02.2012 16:21, 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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--
Matthias Barann
Institute of Clinical Molecular Biology
Christian Albrechts University Kiel
Schittenhelmstr. 12
D-24105 Kiel, Germany
m.barann(a)ikmb.uni-kiel.de
+49 - (0)431 - 597 8681 (office)