Hello all,
Here are the minutes of the Geuvadis analysis group TC of March 8.
The next call will be on March 22.
Action items:
- everyone should upload any missing fastqs that they have ready,
and whatever is not should be produced asap
- Thasso will upload the mRNA bams from GEM that are ready, and
continue mapping the rest of the mRNA data
- Tuuli will analyze EB virus expression in further detail
- Marc F will see if the Barcelona miRNA pipeline can cope with our
~450 samples
- Tuuli will look into producing alternative allele precursor miRNA
reference sequences for mapping those loci that overlap a genetic
variant
- Natalja and Tuuli will finish the genotype file
- Analysis group meeting in Geneva: Tuuli has sent an email about
the registration. The form is in https://docs.google.com/spreadsheet/viewform?formkey=dE1vZEV3ZmlubFBZUkxHMkhXWjVPcmc6MQ
, deadline March 16.
- most of the sequencing data has been uploaded on the ftp site - a
few mRNAs are missing and about 100 miRNAs.
- imputation is done, and our official, final genotype file should
be ready next week
- mRNA analysis:
- Thasso from Barcelona has mapped about 350 samples with GEM
thus far, the rest is running. He'll start uploading the bams to the
ftp site
- Tuuli has mapped the 24 sandbox samples including the
Epstein-Barr virus in the reference (the virus is used in the LCL
transformation). The virus seems to have quite high and variable
expression levels in many of the samples (RPKM 5-60, median 17).
Tuuli will do more analysis to see if we need to include this as a
covariate in the analyses.
- miRNA analysis
- Henk from Leiden presented some results of Leiden's miRNA
samples. About 20% of the reads seem to be from miRNAs, which is not
bad given the quality of the data from the other labs. He also noted
that other small RNA types are also well represented, especially
snoRNAs - we should definitely analyze these as well and not just
focus on the miRNAs
- Marc from Barcelona presented a summary of the Barcelona miRNA
pipeline that can do QC, quantification, novel miRNA and isomir
detection. Marc will test if the pipeline can cope with all of our
samples; alternatively e.g. the Leiden pipeline could be used. Tuuli
will look into producing alternative allele precursor miRNA
reference sequences for mapping those loci that overlap a genetic
variant.
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
-------- Original Message --------
Hello all,
We'll have our biweekly Geuvadis RNAseq analysis group call on
Thursday at 2pm.
Things to discuss:
- sequencing and data submission progress
- mRNA analysis and mapping progress
- miRNA analysis
- Henk will present some stats of the sequencing in Leiden
- Marc F will present the Barcelona miRNA analysis pipeline
The call details are:
Spain
902 125 136
Other countries +34 91 495 18 99
Participants’ Pin-code: 764989*
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