Admin: Istvan Albert

gravatar for Istvan Albert
Istvan Albert ♦♦ 78k
Reputation:
78,170
Status:
Trusted
Location:
University Park, USA
Website:
https://www.ialbert.me/
Scholar ID:
Google Scholar Page
Last seen:
2 days, 13 hours ago
Joined:
9 years, 2 months 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

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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 5 weeks 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 5 weeks 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 5 weeks ago by Istvan Albert ♦♦ 78k
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Comment: C: Gene Set Enrichment Analysis on T-BioInfo
... if you use a regular link to youtube.com the site will recognize it and embed it like so https://www.youtube.com/watch?v=4hFtjwSyffc&feature=youtu.be your link is not recognized because it has that belgian extension `youtu.be` ...
written 5 weeks ago by Istvan Albert ♦♦ 78k
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Comment: C: Gene Set Enrichment Analysis on T-BioInfo
... iframes are not allows, please use full links ...
written 5 weeks ago by Istvan Albert ♦♦ 78k
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Comment: C: Cooperation for scientific project (python, deep learning, image recognition, hi
... This does not sound like potential job offer, hence the type was changed to Forum. ...
written 5 weeks ago by Istvan Albert ♦♦ 78k
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Comment: C: Alignment-free tools (like Kallisto or Salmon): useful for bacterial transcripto
... I would expect them to be more accurate - but also have the limitations there is no ability to detect a new, unannotated feature. I like to align to view the coverages, then evaluate and compare what I see to what I get from kallisto/salmon. ...
written 6 weeks ago by Istvan Albert ♦♦ 78k
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Comment: C: Alignment-free tools (like Kallisto or Salmon): useful for bacterial transcripto
... effective size is typically defined as `transcript length - read length`, but it is applied as subtracting 1/2 read length on each side. now as to the effect of this correction - as always it depends on what exactly is computed and compared. It may have no effect or it could completely change an ou ...
written 6 weeks ago by Istvan Albert ♦♦ 78k
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Answer: A: Alignment-free tools (like Kallisto or Salmon): useful for bacterial transcripto
... I will say that any tool that uses fewer steps is advantageous. Note how in the first case you would need both an alignment and a feature count to quantify - each needs to be run correctly. For example, are you accounting for the so-called size effect when using feature counts? Where shorter tran ...
written 6 weeks ago by Istvan Albert ♦♦ 78k
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Comment: C: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... I was simply reacting to your statement above where you say: > elPrep currently only supports the Illumina format, That is a much more restrictive statement than the second statement that you make in your reply: > but apart from optical duplicate marking, we haven’t encountered any issues b ...
written 6 weeks ago by Istvan Albert ♦♦ 78k

Latest awards to Istvan Albert

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Is There A Lims That Doesn'T Suck?
Commentator 18 days ago, created a comment with at least 3 up-votes. For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Annotate Regions In Bed File With Nearest Downstream Gene
Scholar 27 days ago, created an answer that has been accepted. For A: bam_sort_core problem when bam files be processed by samtools
Good Answer 4 weeks 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 6 weeks ago, created an answer with at least 3 up-votes. For A: How To Grep Largest Contig From A Multi Fasta File
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers
Good Answer 7 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 7 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Epic Question 7 weeks ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this
Good Answer 7 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 9 weeks ago, created an answer that has been accepted. For A: How Do I Convert From Bed Format To Gff Format?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How To Grep Largest Contig From A Multi Fasta File
Librarian 3 months ago, created a post with more than 10 bookmarks. For Table Of Contents To All Review Paper Compilations On Biostar
Great Question 4 months ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Find Unique Reads?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Extracting Reads That Are Properly Paired From Bam File

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