User: Manuel Landesfeind
Manuel Landesfeind • 1.2k
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- Göttingen, Germany
- Last seen:
- 10 months, 3 weeks ago
- Joined:
- 5 years, 2 months ago
- Email:
- l**********@gmail.com
Posts by Manuel Landesfeind
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... Evotec is a leader in the discovery and development of novel small molecule drugs with operational sites in Europe and the US. The Company has built substantial drug discovery expertise and an industrialized platform that can drive new innovative small molecule compounds into the clinic. In addition ...
written 11 months ago by
Manuel Landesfeind • 1.2k
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... [Evotec](https://www.evotec.com/en) is a leader in the discovery and development of novel small molecule drugs with operational sites in Europe and the US. The Company has built substantial drug discovery expertise and an industrialized platform that can drive new innovative small molecule compound ...
written 11 months ago by
Manuel Landesfeind • 1.2k
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... If you have already an R package for the analysis task available and you just want to have some web-interface to make it accessible, a quick alternative might be the development of a [Shiny app][1].
Anyway, for larger and more complex projects, I recommend liux.bio's answer
[1]: https://shiny.r ...
written 2.2 years ago by
Manuel Landesfeind • 1.2k
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... Some time ago I have done a comparison of WES and RNA-Seq variant calling in a setting with more samples (92) but different software (GATK vs. Samtools) for the calling (which might introduce additional bias), but I confirm that the overlap between both methods is rather low. You may want to have a ...
written 2.2 years ago by
Manuel Landesfeind • 1.2k
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... I agree, in that case you should not use tumor as normal. But than I would still go forward with calling mutations on all samples and removing everything found in population databases with decent frequency. ...
written 2.4 years ago by
Manuel Landesfeind • 1.2k
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... About the somatic variants: you can annotate with ExAC (or other population databases) to remove "putative germline" from your analysis. There are plenty of suggestions on Biostars already.
Second, depending on your scientific question, it might be sufficient to use the "tumor" as "normal" because y ...
written 2.4 years ago by
Manuel Landesfeind • 1.2k
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... The term "GRCh38" refers to the genomic assembly. The ".78" and ".91" refer to the version of gene annotation provided by Ensembl, i.e. where do introns/exons/etc start and end. To my knowledge, the genomic sequence for "GRCh38.78" and "GRCh38.91" should be identical and only the gene annotation sho ...
written 2.4 years ago by
Manuel Landesfeind • 1.2k
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... @Asaf already mentioned that the topic is well-studied and I agree that little improvements will have little impact. In particular if you have to demonstrate economic impact in your proposal.
Industry likes de facto standards and well-established and often-used methods. I work in a CRO with all ki ...
written 3.0 years ago by
Manuel Landesfeind • 1.2k
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... Thats interesting... for some reason I thought it would be hg38... don't know why.. ...
written 3.3 years ago by
Manuel Landesfeind • 1.2k
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... What can be discussed is the threshold you use: when do you consider a variant as putative germline? 1%, 10%, ... allelic frequency? In any population or overall?
PS: If you figure out a good threshold or some literature, please share here because it will save me some time to evaluate this by mysel ...
written 3.3 years ago by
Manuel Landesfeind • 1.2k
Latest awards to Manuel Landesfeind
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Influence of RNA-seq read splitting on the BAQ calculation in samtools mpileup
Appreciated
3.0 years ago,
created a post with more than 5 votes.
For C: Stop to make GUI with Java .... Use Qt 5 !!
Appreciated
3.2 years ago,
created a post with more than 5 votes.
For C: Stop to make GUI with Java .... Use Qt 5 !!
Guru
3.4 years ago,
received more than 100 upvotes.
Centurion
3.5 years ago,
created 100 posts.
Scholar
3.9 years ago,
created an answer that has been accepted.
For A: Changing the header of a VCF file and the field correspondingly
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4.1 years ago,
created an answer that was upvoted at least 5 times.
For A: Splice aware aligner - what does it mean?
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4.2 years ago,
created an answer that has been accepted.
For A: Changing the header of a VCF file and the field correspondingly
Scholar
4.2 years ago,
created an answer that has been accepted.
For A: Changing the header of a VCF file and the field correspondingly
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4.6 years ago,
created a post with more than 5 votes.
For C: Stop to make GUI with Java .... Use Qt 5 !!
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4.6 years ago,
created an answer that has been accepted.
For A: Changing the header of a VCF file and the field correspondingly
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4.6 years ago,
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4.7 years ago,
created a comment with at least 3 up-votes.
For C: How to deal with many uncharacterized protein in the blastx results?
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4.7 years ago,
created an answer that has been accepted.
For A: Changing the header of a VCF file and the field correspondingly
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4.8 years ago,
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For C: How to deal with many uncharacterized protein in the blastx results?
Appreciated
4.8 years ago,
created a post with more than 5 votes.
For C: Stop to make GUI with Java .... Use Qt 5 !!
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