Admin: Istvan Albert

gravatar for Istvan Albert
Istvan Albert ♦♦ 79k
Reputation:
78,750
Status:
Trusted
Location:
University Park, USA
Website:
https://www.ialbert.me/
Scholar ID:
Google Scholar Page
Last seen:
2 days, 20 hours ago
Joined:
9 years, 4 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

<prev • 4,600 results • page 2 of 460 • next >
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Answer: A: Set minimum variant frequency while calling variants with samtools
... You can filter your VCF file as it is being produced with `bcf filter` ...
written 9 days ago by Istvan Albert ♦♦ 79k
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Answer: A: How to select SNPs the most conservative way after WGS Variant Calling?
... You could make use of depth and allele frequencies as well. The more samples you have to more difficult is to understand how was the QUAL field computed and what weight it assigns to the data. In addition, you could run a second SNP caller and take the SNPs identified by both more "credible". ...
written 9 days ago by Istvan Albert ♦♦ 79k
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Comment: C: PCAtools: everything Principal Components Analysis
... Oh, I got caught up with "opinions" and forgot the most important message - great library - we were investigating options for PCA plotting this very morning - very timely and thanks for the work! ...
written 10 days ago by Istvan Albert ♦♦ 79k
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Comment: C: PCAtools: everything Principal Components Analysis
... One comment I would have is that I think the package should work off simple text files, rather than spending most of the tutorial code that preparing and formats the data to be readable into the package - and this cuts to almost to the philosophy of how Bioconductor packages are usually presented. ...
written 10 days ago by Istvan Albert ♦♦ 79k
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Answer: A: Strange output of samtools flag stat?
... One lesson that I have learned (the hard way) that it is challenging (sometimes impossible) to precisely reproduce the statistics generated by different tools. Words such as "mapped", "singletons", "total" are not well defined. For example, in this case "what is total?": the number of reads, the n ...
written 24 days ago by Istvan Albert ♦♦ 79k
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News: 2nd Edition of the Biostar Handbook. New online course starts now.
... Two years after the launch, the Biostar Handbook gets a rewrite. The 2nd Edition is a complete rework, every section, chapter and page will be edited, expanded and modernized. https://www.biostarhandbook.com/ A lot has changed in the past two years - the good news is applying tools and techniques ...
biostar handbook news written 25 days ago by Istvan Albert ♦♦ 79k
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Comment: C: How to download raw data in batch from NCBI based on Series Accession number or
... There is an XML file that contains all the information that is displayed, though getting the data out can be somewhat convoluted. For example: esearch -db sra -query SRR1761531 | efetch > summary.xml cat summary.xml | xtract -Pattern SAMPLE_ATTRIBUTE -element TAG,VALUE would produce: ...
written 9 weeks ago by Istvan Albert ♦♦ 79k
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Comment: C: Hidden reads in IGV
... that is a nice summary that covers cases that haven't occurred to me. It is bioinformatics alright ... even simple concepts like read depth and coverage may have many competing definitions. ...
written 12 weeks ago by Istvan Albert ♦♦ 79k
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Comment: C: Hidden reads in IGV
... You cannot add a third column to `samtools depth` it is just not what it was designed to do. I will also say that for high coverage data (like the one you have with a coverage of 124,000x) that also may contain a reads with multiple alignments, duplicates, secondary and supplementary alignments and ...
written 12 weeks ago by Istvan Albert ♦♦ 79k
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Comment: C: Python Data Visualization Course. Last 3 spots left
... Your posts have not been deleted. The site moves fast, lots of content gets generated and your posts will get displaced from the front page. Perhaps it is that event that you feel like "deletion" of posts. Rest assured that people searching for courses will find your posts as Google ranks the site ...
written 12 weeks ago by Istvan Albert ♦♦ 79k

Latest awards to Istvan Albert

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: How Much Of The Genome Will Remain Un-Sequenced At A Given Coverage?
Commentator 5 days ago, created a comment with at least 3 up-votes. For C: Redundant @Sq Lines In Bam File
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Picking A Programming Language And Where To Begin
Great Question 23 days ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Picking A Programming Language And Where To Begin
Great Question 26 days ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Great Question 6 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers
Scholar 9 weeks ago, created an answer that has been accepted. For A: bam_sort_core problem when bam files be processed by samtools
Great Question 10 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Is There A Lims That Doesn'T Suck?
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Annotate Regions In Bed File With Nearest Downstream Gene
Scholar 3 months ago, created an answer that has been accepted. For A: bam_sort_core problem when bam files be processed by samtools
Good Answer 3 months 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

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