Hello,
We'll have a Geuvadis analysis group TC on Thursday 28th at 2pm CET.
On the agenda:
- analysis updates
- wiki
- Liniana's presentation: "Conjoined genes in human populations"
- Mar's presentation: "Ubiquity vs specificity of gene and isoform
expression across populations"
NOTE: Call details different from the usual:
Germany: 0049 692 573 804 41
Spain: 0034 931 816 661
UK: 0044 203 370 57 19
Sweden: 0046 840 309 949
The Netherlands: 0031 108 920 271
Access code: /*611683 */
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
Mar
---------- Forwarded message ----------
From: Mar Gonzàlez-Porta <mar(a)ebi.ac.uk>
Date: 2012/6/21
Subject: Re: [Geuvadis_rna_analysis] Analysis group TC June 21st
To: Natalja Kurbatova <natalja(a)ebi.ac.uk>
Cc: Liliana Greger <lgreger(a)ebi.ac.uk>
Please find attached the slides for today's meeting.
Cheers,
Mar
2012/6/20 Natalja Kurbatova <natalja(a)ebi.ac.uk>
>
>
> -------- Original Message -------- Subject: [Geuvadis_rna_analysis]
> Analysis group TC June 21st Date: Wed, 20 Jun 2012 16:26:36 +0200 From: Tuuli
> Lappalainen <Tuuli.Lappalainen(a)unige.ch> <Tuuli.Lappalainen(a)unige.ch> To:
> geuvadis_rna_analysis(a)lists.crg.es <geuvadis_rna_analysis(a)lists.crg.es><geuvadis_rna_analysis(a)lists.crg.es>
>
> Hello all,
>
> We'll have a Geuvadis RNAseq analysis group TC on Thursday June 21st at
> 2pm CET.
>
> On the agenda:
> - program for the Barcelona meeting (see attached draft)
> - data and analysis updates
> - Jonas from Uppsala will present some QC results
> - Liliana from EBI will present "Conjoined genes in human populations"
> - Mar from EBI will present "Ubiquity vs specificity of gene and isoform
> expression across populations" (if there's time)
>
> Call details are:
> from outside spain; 0034917911859
> from spain; 900800678
> Access code; 3160100
>
> 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)22-3795550tuuli.lappalainen(a)unige.ch
>
>
Hello All,
Please find attached the updates slides which I will present on the today's conference call.
Regards Liliana
Dr. Liliana Greger
EMBL Outstation - Hinxton,
European Bioinformatics Institute,
Wellcome Trust Genome Campus,
Hinxton,
Cambridge, CB10 1SD
Hello all,
We'll have a Geuvadis RNAseq analysis group TC on Thursday June 21st at
2pm CET.
On the agenda:
- program for the Barcelona meeting (see attached draft)
- data and analysis updates
- Jonas from Uppsala will present some QC results
- Liliana from EBI will present "Conjoined genes in human populations"
- Mar from EBI will present "Ubiquity vs specificity of gene and isoform
expression across populations" (if there's time)
Call details are:
from outside spain; 0034917911859
from spain; 900800678
Access code; 3160100
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
Dear All,
These are the slides for the Geuvadis meeting today.
Regards
Liliana
Dr. Liliana Greger
EMBL Outstation - Hinxton,
European Bioinformatics Institute,
Wellcome Trust Genome Campus,
Hinxton,
Cambridge, CB10 1SD
Hello all,
We'll have a Geuvadis analysis group call on Thursday June 7th at 2PM CET.
On the agenda:
- Barcelona meeting arrangements
- data updates: quantifications, genotypes, annotations
- updates from subgroup analyses
- Tuuli will present slides of allele-specific expression analysis
Call details are:
from outside spain; 0034917911859
from spain; 900800678
Access code; 3160100
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
Hello,
Jonas pointed out that the GEM bam files don't have header lines, which
may be a problem in some cases. I uploaded a reference index file
(/upload/geuvadis/wp4_rnaseq/main_project/external_data/reference/hg19_AXYM.fa.fai)
that can be used at least in samtools as additional information so that
header info is not required, or you can also use that to add headers to
your bams if you like.
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 6/18/12 11:29 AM, Jonas Carlsson wrote:
> Hello!
>
> When I tried to run QC-analysis on the GEM-files many of the analysis
> modules failed because there is no header in the .bam-files. Is this a
> mistake or by choice?
>
> /Jonas
Hello all,
The Geuvadis RNAseq genotypes from Phase1 and Phase2 samples are now
available in:
/upload/geuvadis/wp4_rnaseq/main_project/external_data/genetic_variation/genotype/phase1_phase2/
These are vcf files, with a .genotypes.vcf file per chromosome, and a
.sites.vcf file of the whole genome that contains the first 8 columns of
the genotype files with all the variant information. See the header
lines for explanation of the info tags. There's also a sample
information file. In a couple of weeks there will be an update on the
variant annotations.
Phase1 genotypes come from 1000g Phase1 v3 release, and Phase2 genotypes
have been imputed from Omni2.5M - wiki has some more details on this
from Natalja. The imputation results have been filtered as follows; in
the end we have 38,187,570 variants left.
- imputed Phase2 genotypes with bad imputation quality (<0.5) have
missing values. Note that Phase1 genotypes for these variants are
perfectly OK to use in analyses even though the overall missingness rate
is 10%.
- variants with multiple alleles and sites with multiple variants have
been excluded. I noticed that either imputation or the merge of the
Phase1 and Phase2 data messed up some of these sites, so I thought that
the safest thing to do is to remove them - it's not a huge loss and I'm
not sure how reliable these genotype calls are in the Phase 1 anyway.
- Even after these filters, there was a very low number of variants with
very discordant frequencies in Phase1 and Phase2. Most of these seemed
to be variants that are on the Omni2.5M with an allele flip in the
original Phase2 SNP genotypes data that was used in imputation. This is
an ad hoc filter, but I removed 2876 variants with >0.3 frequency
difference between Phase1 and Phase2.
I've done a number of checks on these files, but please let me know if
you observe anything that doesn't seem right. Thanks to Natalja and
Thomas W for all the work for getting these data together.
have a nice weekend!
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
Hello all,
Let's skip this week's Geuvadis RNAseq analysis group TC - the next call
will be in one week, on June 21st at 2pm CET.
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