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@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@unige.ch
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