User: Aerval

gravatar for Aerval
Aerval270
Reputation:
270
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Trusted
Location:
Germany
Last seen:
5 months, 2 weeks ago
Joined:
4 years ago
Email:
r**************@gmail.com

PhD student from Berlin, Germany

Posts by Aerval

<prev • 45 results • page 1 of 5 • next >
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Answer: A: Difference between DNA microarray and RNA microarray
... There isn't such thing as a RNA microarray, its always a DNA microarray (meaning a grid of DNA spots) that is able to measure RNA abundance. It is just that there are also DNA arrays for other sample types like methylation or genotyping ...
written 6 months ago by Aerval270
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Comment: C: Multisample DMR calling
... Thanks, that looks interesting. I am not working on that particular project anymore but will forward your link to the people still working on it. ...
written 7 months ago by Aerval270
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Job: PhD student position in bioinformatics (sequence analysis, functional genomic, data mining, ML) at BIH, Berlin, Germany
... We are looking for a PhD student in computational biology/bioinformatics who will join Martin Kircher’s Junior Research Group at the Berlin Institute of Health in Germany. Starting date is January 1st, 2018 or later. The group does research in the areas of **sequence analysis, data mining and functi ...
machine learning genomics variant effect mpra job written 7 months ago by Aerval270
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Comment: C: Survey/Vote: If you could double the speed of any three commandline tools, which
... I wondered, would a linear sorting algorithm like radixsort improve that or are indexing and later random accessing the sorted lines the bottle neck. I mean, formats like bed or vcf have nicely defined columns that need to be sorted most of the times. ...
written 7 months ago by Aerval270
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Answer: A: Threshold for Differentially Methylated Regions
... You cannot set a definitive threshold when change in methylation is meaningful. Sure, a single cell is always 1, 0.5 or 0 methylated at one site, but you have bulk data from probably thousands of cells. Statistical tests are for sure the way to go but differ (depending on your type of data and some ...
written 13 months ago by Aerval270
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Answer: A: Bisulfite sequencing query
... You wont get a definite answer here as there is not that BS protocol, there is WGBS, RRBS, 450/850k arrays that are equally important. A good introduction will be Christoph Bocks review: http://www.nature.com/nrg/journal/v13/n10/full/nrg3273.html ...
written 15 months ago by Aerval270
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Comment: C: CpG Island prediction
... I do not have an overview over the field and therefore cannot add much but would suggest not to look at omictools.com. Their list is almost certainly incomplete and outdated like in this case where the three tools labelled "new" (including newcpgreport and cpgplot) are from 1999, 1999 and 1992! That ...
written 15 months ago by Aerval270
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Comment: C: CpG coverage of BS-seq ?
... Sorry if I misused the term dinucleotide, I meant both cytosines in a CpG double strand site. So one CpG. ...
written 15 months ago by Aerval270
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Answer: A: CpG coverage of BS-seq ?
... CpG usually means the CpG dinucleotide (and is afaik specified otherwise if not). When you use bsseqs `getCov` you get the number of + and - strand reads. (I have no idea about RRBS as I am working with WGBS) ...
written 15 months ago by Aerval270
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Comment: C: Looking for a Bioinformatics Internship in Europe
... Hey Nephtali, I think you need to specify your interest more. Bioinformatics is a broad field and there are hundereds of groups in Europe (in academia, you are not specifying whether you want to go there or into industry), you might get a contact through this but honestly I in your position would r ...
written 16 months ago by Aerval270

Latest awards to Aerval

Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Advice for undergraduate bioinformatics learners
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Advice for undergraduate bioinformatics learners
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.

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