Admin: Istvan Albert

gravatar for 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 sciencemachine learninguser 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:

Posts by Istvan Albert

<prev • 4,581 results • page 1 of 459 • next >
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Comment: C: What would be the trend in next few years in NGS era?
... 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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Answer: A: bam_sort_core problem when bam files be processed by samtools
... 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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Comment: C: Antisense transcription from strand specific RNA-seq
... 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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Answer: A: Antisense transcription from strand specific RNA-seq
... 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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Comment: C: What is the minimum system requement for oxford nanopore read assembly
... 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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Comment: C: What is the minimum system requement for oxford nanopore read assembly
... 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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Comment: C: Illumina to Acquire Pacific Biosciences
... 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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News: Illumina to Acquire Pacific Biosciences
... 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 ...
illumina news pacbio written 15 days ago by Istvan Albert ♦♦ 78k
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Comment: C: RNA-Seq analysis = only 10 DE genes
... 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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Answer: A: RNA-Seq analysis = only 10 DE genes
... 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

Latest awards to Istvan Albert

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Annotate Regions In Bed File With Nearest Downstream Gene
Scholar 5 days ago, created an answer that has been accepted. For A: bam_sort_core problem when bam files be processed by samtools
Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: How To Grep Largest Contig From A Multi Fasta File
Commentator 26 days ago, created a comment with at least 3 up-votes. For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Great Question 4 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Epic Question 4 weeks ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How Do I Convert From Bed Format To Gff Format?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How To Grep Largest Contig From A Multi Fasta File
Librarian 12 weeks ago, created a post with more than 10 bookmarks. For Table Of Contents To All Review Paper Compilations On Biostar
Great Question 3 months ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Find Unique Reads?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Extracting Reads That Are Properly Paired From Bam File
Popular Question 4 months ago, created a question with more than 1,000 views. For Jonathan Pevsner author of Bioinformatics and Functional Genomics uses this
Great Question 4 months ago, created a question with more than 5,000 views. For Hadley Wickham of ggplot and RStudio uses this
Epic Question 4 months ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this

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