User: Istvan Albert

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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Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.

... Yes, this is my priority as well, I will do my best to rework the Coronavirus chapter by mid-February. The plan is that by the end of the month the RNA-Seq book will gain a chapter, the "Grouchy Grinch RNA-Seq", where I cover data where RNA-Seq analysis can go radically off-track and what to do a ...

written 6 weeks ago by Istvan Albert ♦♦ 86k

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Comment: C: What does p-value mean ? What and how can i interpret the results

... the phrase "due to chance" has no connection to the magnitude of the p-values at all. Observing smaller or larger probability does not affect the interpretation of the second part of the sentence. "due to chance" is just a succinct way to say "caused by random chance while the null hypothesis is ...

written 6 weeks ago by Istvan Albert ♦♦ 86k

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Answer: A: What does p-value mean ? What and how can i interpret the results

... There is a tradeoff. When we try to be precise, the explanations become a little unwieldy and make the definition hard to remember. When we make the explanation simple, the wording is ambiguous. Here is a definition that I like, tries to reconcile the two extremes: > The p-value is the proba ...

written 6 weeks ago by Istvan Albert ♦♦ 86k

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Comment: C: NGS RNA-Seq Analysis Pipeline Tophat vs STAR

... I think it is fine, I don't want to mess with the nice guide there. A minor oversight at most. ...

written 7 weeks ago by Istvan Albert ♦♦ 86k

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Comment: C: NGS RNA-Seq Analysis Pipeline Tophat vs STAR

... Forum is the more appropriate type. Conceptually blog posts are the content in the PLANET blog aggregator and using them in both contexts may end up as confusing. The Blog type should not be selectable in the dropdown, it is just an oversight. ...

written 7 weeks ago by Istvan Albert ♦♦ 86k

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Answer: A: mRNA Translation: TGG/UGG as a start codon?

... Ah, the first time I get to demonstrate my cool new software to the world :-) I've designed it exactly to explore these types of problems. I understand the author already figured out the answer, this is more a demonstration for the next person with the same problem of what they could do to figure ou ...

written 7 weeks ago by Istvan Albert ♦♦ 86k

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Comment: C: How minimap2 mapping works

... Do you want reads to match to the location that they are most similar to or do you want to ensure that they only match to one organism (reference?). Choose depending on the goals you have. ...

written 8 weeks ago by Istvan Albert ♦♦ 86k

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Answer: A: Create a single fastq ids in each row

... assuming your input is in a file called `ids` you can use the UNIX command line tool called `tr` to transform commas into newlines like so: cat ids | tr ',' '\n' | head prints: A00868:56:HK2YWDRXX:1:2103:1832:17472 A00868:56:HK2YWDRXX:1:2106:21775:8547 A00868:56:HK2YWDRXX:1:2113: ...

written 8 weeks ago by Istvan Albert ♦♦ 86k

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Answer: A: paired-end fastq file remove mismatching lengths of bases and qualities error

... You have multiple different errors, note how the first error says: * There appear to be different numbers of reads in the paired input files. whereas the second error is * Mismatch between length of bases and qualities for read 107893745 your data seems to have multiple, overlapping problems I ...

written 8 weeks ago by Istvan Albert ♦♦ 86k

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Comment: C: RNA-seq snp discovery use bcftools

... bcftools is a software that (among the many features) allows you to generate and filter variants. The process you have to follow is not running someone else's code that you don't understand. Instead study that code, understand what it does, then apply the parameters yourself. In your case run `bcf ...

written 8 weeks ago by Istvan Albert ♦♦ 86k

Latest awards to Istvan Albert

Epic Question 1 day ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this

Scholar 1 day ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll

Great Question 8 days ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this

Commentator 22 days ago, created a comment with at least 3 up-votes. For C: Suggesting The Removal Of Post Closing

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Pablo Cingolani of snpEff uses this

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll

Appreciated 9 weeks ago, created a post with more than 5 votes. For bam.iobio realtime sampling to generate global statistics of your bam file in a few seconds

Epic Question 11 weeks ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this

Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll

Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Suggesting The Removal Of Post Closing

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll

Popular Question 3 months ago, created a question with more than 1,000 views. For Pablo Cingolani of snpEff uses this

Great Question 3 months ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this

Scholar 3 months ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll

Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: bwa mem and multiply mapped reads

Scholar 4 months ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?

Appreciated 4 months ago, created a post with more than 5 votes. For bam.iobio realtime sampling to generate global statistics of your bam file in a few seconds

Scholar 4 months ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll

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