Admin: Istvan Albert
Istvan Albert ♦♦ 78k
- Reputation:
- 77,900
- Status:
- Trusted
- Location:
- University Park, USA
- Website:
- https://www.ialbert.me/
- Scholar ID:
- Google Scholar Page
- Last seen:
- 14 hours ago
- Joined:
- 9 years, 1 month ago
- Email:
- i************@gmail.com
I have published research works in the fields of granular matter physics, network science, machine learning, user interfaces and bioinformatics. But above all I like to create useful systems. I enjoy the process of designing and implementing web based services that stand the test of time. My current project that I dedicate most my time to is an e-book on genomic data analysis:
- The Biostar Handbook - it is modeled by the content on this site and is a comprehensive guide for beginning bioinformaticians.
I am the maintainer of this site:
- Biostar Q&A platform more of a jack-of-all-trades: lead developer, interface designer, database manager, sys admin, dev-ops etc. whatever needs to be done.
Currently I work as a Professor of Bioinformatics at Penn State. Within that position I serve in various roles:
- Director of the Bioinformatics Consulting Center at Penn State
- Bioinformatics instructor
- Researcher and tool developer GeneTrack, and a few others
Posts by Istvan Albert
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... I do agree. Long reads are game-changing in more than one way.
For most people bioinformatics today is a narrow concept, it really means dealing with the various constraints that billions of short reads impose on us. What changes when we have few but long reads? ... Well ... everything.
right off ...
written 3 days ago by
Istvan Albert ♦♦ 78k
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... These are not error messages, just debugging notes.
Large files cannot be sorted in memory thus get saved into temporary files. Once the sort completes the temporary files are removed.
There is nothing to be concerned about ...
written 5 days ago by
Istvan Albert ♦♦ 78k
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... This is a good point - but this is more of a final solution that one aspires to once they get a firm understanding of the processes that take place. I will make this into a recipe as well.
I will say that in general one should start out by splitting the files, visualizing and understanding what eac ...
written 8 days ago by
Istvan Albert ♦♦ 78k
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... I am creating a recipe called "Anti Sense Transcripts" as a teaching aid:
As of today (November 8, 2018) I am still exploring the best way to make the point but I think it is already useful.
Look at the code for the guidance of what each step does. Also the results will allow you to visualize t ...
written 9 days ago by
Istvan Albert ♦♦ 78k
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... Cluster computing facility is actually no help here. A typical cluster architecture is designed to provide lots of CPU nodes but cannot give you more memory than what a given node already has. ...
written 15 days ago by
Istvan Albert ♦♦ 78k
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... I would say that the answer will depend on more what you are assembling (complexity of size or population) ...
written 15 days ago by
Istvan Albert ♦♦ 78k
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... inventors don't make for good business people, take the MinION as an example. Great technology - cool concept, inefficiently run as a business and still languishing. ...
written 15 days ago by
Istvan Albert ♦♦ 78k
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5 follow
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... In the news:
[Illumina to Acquire Pacific Biosciences for Approximately $1.2 Billion, Broadening Access to Long-Read Sequencing and Accelerating Scientific Discovery][news]
It is interesting to consider what this means - is short read sequencing on the downtrend? Or is a business move to limit Pa ...
written 15 days ago by
Istvan Albert ♦♦ 78k
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210
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... The best is to align separately against the genome, you can use hisat2 or even bwa mem for that.
If your samples are similar across samples it means there is no expression change. Correlation may not be informative in some cases where lengthy well-correlated regions will mask shorter, uncorrelated ...
written 15 days ago by
Istvan Albert ♦♦ 78k
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210
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... Always visualize your results with other means, in this case align against the genome. Once you look at your data with IGV the answers will be more forthcoming.
Are you getting so few results because the data is perfect, everything comes out the same across all samples? (this is usually rare)
Then ...
written 16 days ago by
Istvan Albert ♦♦ 78k
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