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: 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 5 weeks ago by Istvan Albert ♦♦ 78k

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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 8 weeks ago by Istvan Albert ♦♦ 78k

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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 8 weeks ago by Istvan Albert ♦♦ 78k

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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 8 weeks ago by Istvan Albert ♦♦ 78k

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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 9 weeks 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 9 weeks 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 9 weeks 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 weeks 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 10 weeks 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 10 weeks ago by Istvan Albert ♦♦ 78k

Latest awards to Istvan Albert

Popular Question 9 days ago, created a question with more than 1,000 views. For bam.iobio realtime sampling to generate global statistics of your bam file in a few seconds

Great Question 11 days ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this

Popular Question 13 days ago, created a question with more than 1,000 views. For bam.iobio realtime sampling to generate global statistics of your bam file in a few seconds

Popular Question 16 days ago, created a question with more than 1,000 views. For bam.iobio realtime sampling to generate global statistics of your bam file in a few seconds

Commentator 16 days ago, created a comment with at least 3 up-votes. For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers

Scholar 4 weeks ago, created an answer that has been accepted. For A: bam_sort_core problem when bam files be processed by samtools

Appreciated 4 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

Popular Question 5 weeks ago, created a question with more than 1,000 views. For bam.iobio realtime sampling to generate global statistics of your bam file in a few seconds

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

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Is There A Lims That Doesn'T Suck?

Appreciated 7 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

Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Annotate Regions In Bed File With Nearest Downstream Gene

Scholar 9 weeks ago, created an answer that has been accepted. For A: bam_sort_core problem when bam files be processed by samtools

Good Answer 10 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

Popular Question 10 weeks ago, created a question with more than 1,000 views. For bam.iobio realtime sampling to generate global statistics of your bam file in a few seconds

Appreciated 12 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

Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How To Grep Largest Contig From A Multi Fasta File

Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers

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

Epic Question 3 months ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this

Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Where To Look For Quality Bioinformatics Short Courses And Workshops?

Appreciated 3 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

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