SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 68
Search took 0.01 seconds.
Search: Posts Made By: Robby
Forum: Bioinformatics 07-10-2018, 05:45 AM
Replies: 0
Views: 619
Posted By Robby
Gene set enrichment analysis for Drosophila

Hi everybody,

I would like to use the functions goana and kegga from limma package to perform gene set enrichment analyses for Drosophila. Does anybody know whether the p-value in the results is...
Forum: Academic/Non-Profit Jobs 06-20-2017, 08:00 AM
Replies: 0
Views: 668
Posted By Robby
PhD or PostDoc position: Computational Microbiology in Kiel, Germany

Research Group Medical Systems Biology, Institute of ExperimentalMedicine/Christian Albrechts University of Kiel (CAU)
The University Medical Center Schleswig-Holstein is one of the largest...
Forum: Academic/Non-Profit Jobs 04-25-2017, 12:34 AM
Replies: 0
Views: 756
Posted By Robby
PhD position in Systems Biology of Inflammation

The research group “Medical Systems Biology” at the University Medical Center Schleswig-Holstein (Kiel, Germany) seeks for a motivated PhD.

Your role: Supporting our interdisciplinary research...
Forum: Bioinformatics 10-03-2015, 08:35 AM
Replies: 6
Views: 3,301
Posted By Robby
OK, that seems to work. I have still some...

OK, that seems to work. I have still some warnings, but at least no errors. So I will start to test, if it really works. Thanks a lot for your help

Building Bio-SamTools
gcc...
Forum: Bioinformatics 10-03-2015, 07:20 AM
Replies: 6
Views: 3,301
Posted By Robby
Thanks for your prompt answers! I tested...

Thanks for your prompt answers!

I tested your comand first with samtools 0.1.17 and afterwards with samtools 1.2:


$ SAMTOOLS='/path/samtools-0.1.17'
$ echo $SAMTOOLS...
Forum: Bioinformatics 10-03-2015, 12:12 AM
Replies: 6
Views: 3,301
Posted By Robby
Yes, I applied the following command export...

Yes, I applied the following command
export SAMTOOLS=$SAMTOOLS:/path/samtools
Forum: Bioinformatics 10-02-2015, 12:20 PM
Replies: 6
Views: 3,301
Posted By Robby
Installation problems Bio-SamTools

Hi everybody,

I would like to install Bio-SamTools 1.41 without root-permissions. I tried the following commands:
perl Build.PL --install_base /home/$User/perl5
./Build

But I received the...
Forum: Bioinformatics 07-21-2015, 10:05 AM
Replies: 1
Views: 1,553
Posted By Robby
alternative for HTSeq

Hello,
We sequenced RNA for one organism with a very incomplete reference sequence. So we had to map against nearly 6000 contigs. Nevertheless we would like to investigate differentially expressed...
Forum: Bioinformatics 05-10-2015, 02:11 AM
Replies: 0
Views: 907
Posted By Robby
Annovar -> SIFT scores

Hi everybody,

I received variant data, which were annotated with Annovar (version 2013). If I see it correctly, the SIFT score is classified as deleterious for values >=0.95. But on the hompage...
Forum: Bioinformatics 05-10-2015, 02:01 AM
Replies: 2
Views: 1,388
Posted By Robby
OK thanks. I used the the following command to...

OK thanks. I used the the following command to install R:
sudo apt-get install r-base
I thought that will install the newest R version. But this was not the case. Now I managed to install the...
Forum: Bioinformatics 05-08-2015, 09:07 AM
Replies: 2
Views: 1,388
Posted By Robby
DESeq2 version problems

Hello,

How can I receive the newest version of DESeq2 for Ubuntu? I have the following problem:

I had to change my computer. On both computer R version 3.02 is installed on a Linux system. On...
Forum: Bioinformatics 02-25-2015, 06:04 AM
Replies: 0
Views: 887
Posted By Robby
KEGG enrichment analysis mouse

Hello everybody,

I have a list of gene symbols from differently expressed genes from mouse data. We would like to perform KEGG (not GO!) enrichment analysis. Unfortunately most of the tools are...
Forum: Bioinformatics 07-06-2014, 12:54 AM
Replies: 11
Views: 8,578
Posted By Robby
Hello, I have a problem to understand the...

Hello,
I have a problem to understand the Pindel output for deletions, if the deletion is not 'pure'. For example:

279 D 24 NT 16 "GAAGAGAAGAGACAAG" ChrID chr5 BP 145645795 ...
Forum: Bioinformatics 07-06-2014, 12:23 AM
Replies: 2
Views: 1,377
Posted By Robby
Just use any date. I think a proper vcf file...

Just use any date. I think a proper vcf file needs a header line like "##fileDate=26_Jun_2014". As long as you know, that the date might be wrong and you use the vcf just for your own analysis, it...
Forum: Bioinformatics 07-01-2014, 10:59 AM
Replies: 1
Views: 732
Posted By Robby
I found on the UCSC hompage, that the range is...

I found on the UCSC hompage, that the range is between -20 and 7.528. But I still don't know, when a score is called conserved and if there are better possibilities to decide the conservation
Forum: Bioinformatics 07-01-2014, 10:38 AM
Replies: 1
Views: 732
Posted By Robby
phyloP60way

Hi everybody,

I would like to add PhyoP-scores to my SNVs (organism: mouse). I downloaded the following annotations:
...
Forum: RNA Sequencing 06-15-2014, 10:45 PM
Replies: 4
Views: 6,202
Posted By Robby
Hi, with help of strand specific RNA-Seq...

Hi,

with help of strand specific RNA-Seq you can analyse, which strand was transcribed. This depends on the information to which strand a read maps and if it is the first or second read of the...
Forum: Bioinformatics 04-03-2013, 08:36 AM
Replies: 1
Views: 4,335
Posted By Robby
GATK HaplotypeCaller memory problem

Hello everyone,

I would like to use GATK v2.3.9 for variant calling. But unfortunally the Haplotype Caller fails with the following error message:

I used the following command for the...
Forum: Bioinformatics 01-22-2013, 01:45 AM
Replies: 7
Views: 4,498
Posted By Robby
Is there any tool, which predicts for each...

Is there any tool, which predicts for each variant the probability, that this variant is damaging (like SIFT or PolyPhen for human). As far as I understand snpEff it just shows you the region of the...
Forum: Illumina/Solexa 04-03-2012, 04:17 AM
Replies: 19
Views: 12,699
Posted By Robby
OK, I found the answer: The cluster density will...

OK, I found the answer: The cluster density will not change after cycle 4, so the final cluster density is the same like the 4th cycle cluster density.
Forum: Illumina/Solexa 04-03-2012, 01:53 AM
Replies: 19
Views: 12,699
Posted By Robby
Thanks Philip. You wrote, that after the 4th...

Thanks Philip. You wrote, that after the 4th cycle another cluster density determination is made. Is that cluster density the same as written in the final run statistics? Or where can we find the...
Forum: Illumina/Solexa 03-31-2012, 12:44 AM
Replies: 19
Views: 12,699
Posted By Robby
Hello everyone, I have a look for the...

Hello everyone,

I have a look for the cluster densities for the first time. Do you use for the cluster density the number out of the first base report or the cBot number or any other source? I am...
Forum: Bioinformatics 03-30-2012, 01:48 AM
Replies: 2
Views: 1,735
Posted By Robby
Thanks a lot. That worked perfectly :).

Thanks a lot. That worked perfectly :).
Forum: Bioinformatics 03-29-2012, 06:26 AM
Replies: 2
Views: 1,735
Posted By Robby
mpileup -- bases missing

Hello everyone,
I created with with samtools a mpileup file out of a bam file, but some bases at the beginning and the end are missing in the mpileup, although the bases are covered by a few reads...
Forum: Illumina/Solexa 03-01-2012, 04:56 AM
Replies: 4
Views: 14,563
Posted By Robby
@NextGenSeq: You will need a cBot for the HighSeq...

@NextGenSeq: You will need a cBot for the HighSeq 2500 High Output run (http://www.illumina.com/systems/hiseq_systems.ilmn)

Does anybody have any information about the costs for a HiSeq 2500 run...
Showing results 1 to 25 of 68

 


All times are GMT -8. The time now is 03:42 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO