User: Michael Dondrup

Reputation:
10
Status:
New User
Location:
Bergen, Norway
Last seen:
2 years ago
Joined:
4 years, 4 months ago
Email:
m*******@googlemail.com

I am a researcher at the Sea Lice Research Centre and the Department of Informatics/CBU at the University of Bergen, Norway. I am developing LiceBase, a database for genomics data of sea lice and other emerging genomes. I have a doctoral degree in Bioinformatics and a Diploma in  "Computer Science in the Natural Sciences" with focus on CS, language processing and biology from Bielefeld University, Germany. Have some 'long-standing' (say 30 years+) relationship with programming and cs; it all started when I found a book on BASIC programming for the Commodore PET as a kid :)

Posts by Michael Dondrup

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Warning: missing reverse strand option in easyRNASeq.
... Hi Hervé, thank you for your reply, I have now re-counted all our files using featureCounts (stand-alone executable) and a few also using HTseq-count. The result is reproducibly overall: easyRNAseq with stranded=TRUE and featureCount -s1 deliver ~5% reads assigned to gene models, counting reverse st ...
written 2.4 years ago by Michael Dondrup10
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Answer: A: Is there a reverse strand option in easyRNAseq or is it automatic?
... I have done a comparison using the featureCounts program, seemingly the worst-case scenario happened. The number of assigned reads in featureCounts using -s 2 is on average 10x-15x higher per sample. So it seems that all our counts on recent stranded Illumina data could be wrong! This is possibly a ...
written 2.4 years ago by Michael Dondrup10
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Warning: missing reverse strand option in easyRNASeq.
... I have some relatively recent strand specific RNA-seq data which comes as 'second-strand', that means all reads are reversed with respect to the genomic sequence of the transcript and annotation. With featureCounts I would have to use -s 2 option, for example, to get a 70+% rate of assignments to tr ...
rnaseq easyrnaseq strand written 2.4 years ago by Michael Dondrup10 • updated 2.4 years ago by Hervé Pagès ♦♦ 14k
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Comment: C: Severe problems with bioc installation of source packages (R 3.3 epel)
... Thanks I will try that. ...
written 3.4 years ago by Michael Dondrup10
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Comment: C: Severe problems with bioc installation of source packages (R 3.3 epel)
... Hello Michael Dondrup! We believe that this post does not fit the main topic of this site. This is not a Bioconductor problem but incompatibility of R 3.3 and CentOS 6 For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help ...
written 3.4 years ago by Michael Dondrup10
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Answer: A: Severe problems with bioc installation of source packages (R 3.3 epel)
... Warning: R 3.3.0 doesn't configure or build on CentOS 6.8, and the the Epel package is dysfunct due to this, so if you are running R 3.2, don't upgrade.  From the Cran NEWS:  DEPRECATED AND DEFUNCT The previously included versions of zlib, bzip2, xz and PCRE have been removed, so suitable e ...
written 3.4 years ago by Michael Dondrup10
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Comment: C: Severe problems with bioc installation of source packages (R 3.3 epel)
... Indeed it looks a bit weird, I tried R CMD SHLIB. I guess i need to inform the epel folks, looks like the package is broken. gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules ...
written 3.4 years ago by Michael Dondrup10
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Comment: C: Severe problems with bioc installation of source packages (R 3.3 epel)
... R is installed from the Epel repository directly, not built from source: * epel: fedora.uib.no Installed Packages Name : R Arch : x86_64 Version : 3.3.0 Release : 5.el6 Size : 0.0 Repo : installed From repo : epel Summary : A language for data analysis an ...
written 3.4 years ago by Michael Dondrup10
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Comment: C: Severe problems with bioc installation of source packages (R 3.3 epel)
... Thanks Dan, libcurl-devel is installed already, likewise all other apparently missing libs, including zlib devel which is needed by a lot of other builds. I don't have sudo permission on that machine. Admins asked me to figure out and summarize all dependencies once, before attempting a new instal ...
written 3.4 years ago by Michael Dondrup10
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(Closed) Severe problems with bioc installation of source packages (R 3.3 epel)
... I am experiencing probs installing several source Bioconductor packages on R 3.3.0 on CentOS. Trying to install e.g. packages impute and preprocess core. Details below.  I have seen several recent reports of this error with the same error messages and same missing libraries. Did anyone else experien ...
software error installation written 3.4 years ago by Michael Dondrup10

Latest awards to Michael Dondrup

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Several issues with the package easyRNASeq
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Severe problems with bioc installation of source packages (R 3.3 epel)
Scholar 4.4 years ago, created an answer that has been accepted. For A: Several issues with the package easyRNASeq
Scholar 4.4 years ago, created an answer that has been accepted. For A: Several issues with the package easyRNASeq
Autobiographer 4.4 years ago, has more than 80 characters in the information field of the user's profile.

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