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Forum: Core Facilities 07-24-2013, 02:05 AM
Replies: 16
Views: 9,676
Posted By oliviera
Here is the service we propose to the community, ...

Here is the service we propose to the community,

http://www.itg.kit.edu/ngs.php
(Web site adress is updated and the previous link is now dead)
We are small but responsive!
;)

Cheers
Olivier
Forum: RNA Sequencing 01-04-2013, 05:36 AM
Replies: 4
Views: 2,826
Posted By oliviera
Dear community, dear sdriscoll, I have a...

Dear community, dear sdriscoll,
I have a question which could be a related with cuffdiff.
By comparing the output from isoform_exp.diff and gene_exp.diff it looks like their is less trasnscripts...
Forum: Bioinformatics 10-20-2012, 01:41 AM
Replies: 0
Views: 849
Posted By oliviera
Dispertion RNAseq cummeRbund

Dear all,
I have anaylsed a RNAseq dataset with triplicates and 2 conditionsat the level of differential gene expression with HTSeq and this worked well (make biological sens and candidates...
Forum: Bioinformatics 10-20-2012, 12:53 AM
Replies: 20
Views: 10,428
Posted By oliviera
Only 92 with adjp < 0.01. With DEseq I get...

Only 92 with adjp < 0.01.
With DEseq I get ~2000 genes at this cut off. I think I made something wrong
Forum: Bioinformatics 10-18-2012, 02:00 AM
Replies: 20
Views: 10,428
Posted By oliviera
Hi Alejandro, Here is the graph to check...

Hi Alejandro,

Here is the graph to check dispersion estimate. What do you think?

meanvalues<- rowMeans(counts(ecs))
plot(meanvalues, fData(ecs)$dispBeforeSharing, log="xy", main="mean vs CR...
Forum: Bioinformatics 10-18-2012, 12:39 AM
Replies: 20
Views: 10,428
Posted By oliviera
Dear all, I try to use DExseq but got the...

Dear all,
I try to use DExseq but got the following error when I call the function

ecs<- fitDispersionFunction(ecs)

Warning message:
In glmgam.fit(mm, disps[good], coef.start = coefs) :
...
Forum: Illumina/Solexa 09-23-2012, 11:20 PM
Replies: 27
Views: 9,727
Posted By oliviera
Hi Jessie, In your case I also find the error...

Hi Jessie,
In your case I also find the error Doxygen not found. Not sure what it is but the compilation fail probably because of this error. Install Doxygen first on your system and then compile...
Forum: Core Facilities 07-02-2012, 06:56 AM
Replies: 16
Views: 9,676
Posted By oliviera
We opened last year but are visible on public...

We opened last year but are visible on public only since few months. We have very good expertize in RNAseq and made already successfull run for small RNAseq.

Have a look at...
Forum: Core Facilities 07-02-2012, 01:28 AM
Replies: 0
Views: 1,835
Posted By oliviera
Opening of the EZRC core facility

Dear community,

We are very glad to announce the opening of the NGS facility of the European Zebrafish Ressource Center in Karlsruhe, Germany.
As an Academic lab and core Facility our prices are,...
Forum: Bioinformatics 05-11-2012, 03:03 AM
Replies: 24
Views: 21,339
Posted By oliviera
I am getting the same problem by using: ...

I am getting the same problem by using:
MarkDuplicates.jar
Using LENIENT also goes through.

Did someone look at the original question: is it a bug in bwa?
I try to repeat the pipeline...
Forum: Bioinformatics 05-05-2012, 07:03 AM
Replies: 17
Views: 4,187
Posted By oliviera
It make a lot f sense, indeed. Thanx for you fast...

It make a lot f sense, indeed. Thanx for you fast reply
:)

Olivier
Forum: Bioinformatics 05-05-2012, 03:19 AM
Replies: 17
Views: 4,187
Posted By oliviera
total number of counts with HTseq

Dear all,

I use HTseq with paired end data and would like to calculate the pourcentage of reads that do fall into an annotated genes. To do this I thought to add all count inside genes +...
Forum: Bioinformatics 02-02-2012, 01:40 AM
Replies: 46
Views: 29,570
Posted By oliviera
multiple mapped miRNA with HTseq/DEseq

Dear Simon,
I hope this thread will still find you well.
I am mapping reads from small RNAseq and would like to use HTseq/ DEseq. As miRNA map very often to more than one genomic location I would...
Forum: Bioinformatics 10-12-2011, 12:39 AM
Replies: 3
Views: 9,292
Posted By oliviera
Dear Jon, Which package would you suggest as an...

Dear Jon,
Which package would you suggest as an alternative? I am not convince I can use DESeq or EdgeR with paired end data. What do you think?

Olivier
Forum: Illumina/Solexa 07-21-2011, 06:30 AM
Replies: 27
Views: 9,727
Posted By oliviera
Hi again, I simply reinstall the newest version...

Hi again,
I simply reinstall the newest version of cmake 2.8.5. Should be ok now.
Cheers
olia
Forum: Illumina/Solexa 07-21-2011, 04:47 AM
Replies: 27
Views: 9,727
Posted By oliviera
Dear roko-t I encounter the same problem that...

Dear roko-t
I encounter the same problem that you do to install casava1.8
Could you share with me how you did configure cmake, thats would help a lot

Cheers
Forum: De novo discovery 05-11-2011, 04:01 AM
Replies: 58
Views: 50,344
Posted By oliviera
Thanx for your fast reply, I download and...

Thanx for your fast reply,
I download and install without problem velvet 1.1.03 with
make 'MAXKMERLENGTH=57' 'BIGASSEMBLY=1' 'OPENMP=1'

By ther way I have 76bp paired end reads so I thought it...
Forum: De novo discovery 05-10-2011, 07:21 AM
Replies: 58
Views: 50,344
Posted By oliviera
dear Jenzo, dear All, I have the same...

dear Jenzo, dear All,

I have the same problem than you Jenzo: Oases crashes with the same error that you describe. I guess it is better to use the last release of velvet. Have you managed to use...
Forum: Bioinformatics 05-10-2011, 06:08 AM
Replies: 13
Views: 4,529
Posted By oliviera
Dear all, I have a similar concern. I get ...

Dear all,
I have a similar concern. I get 119021 transcripts model
In my case we have generate > 200 Million paired end reads so coverage should be high.
Have you managed to tune your...
Forum: Bioinformatics 11-17-2010, 03:29 AM
Replies: 7
Views: 3,831
Posted By oliviera
I just tested the new release 1.1.4 and now the...

I just tested the new release 1.1.4 and now the problem seems to be fixed!
Thanx a lot
:)

Oliviera
Forum: Bioinformatics 11-17-2010, 03:03 AM
Replies: 7
Views: 3,831
Posted By oliviera
I have the same problem with tophat 1.1.3, and do...

I have the same problem with tophat 1.1.3, and do not manage to solve the problem.

I used :
./tophat --solexa1.3-quals --no-novel-juncs -G Danio_rerio.Zv9.60.gtf -o /5cq15 Danio_rerio.Zv9.60...
Forum: General 10-15-2010, 04:08 AM
Replies: 2
Views: 2,593
Posted By oliviera
coverage required

Dear all,

I try to get an idea of the base coverage required for the different sequencing applications.
I didn t find any review on this subject so if you know a nice paper or can complete the...
Forum: RNA Sequencing 07-13-2010, 03:35 AM
Replies: 0
Views: 2,498
Posted By oliviera
Tophat: some .sam files empty and some not

Dear All,

I am running tophat on 7 datasets of 76bp paired end reads.
In one case the accepted_hits.sam file is empty while the 6 others are looking good. The fastq file this particular...
Forum: Bioinformatics 07-13-2010, 03:22 AM
Replies: 34
Views: 16,437
Posted By oliviera
Dear Winfred, I think I got a smiliar to...

Dear Winfred,

I think I got a smiliar to yours.
Please a look to this threads and tell me if this is relevant to your problem....
Forum: RNA Sequencing 06-08-2010, 11:49 PM
Replies: 2
Views: 4,646
Posted By oliviera
Dear sjm, Thanx for your answer. I will try...

Dear sjm,

Thanx for your answer. I will try to do as you say. I am not sure of it, but I thought that providing the gff file to tophat will help the mapping of the reads, that s why I thought to ...
Showing results 1 to 25 of 31

 


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