Admin: Istvan Albert

gravatar for Istvan Albert
Istvan Albert ♦♦ 84k
Reputation:
84,180
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Location:
University Park, USA
Website:
https://www.ialbert.me/
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Google Scholar Page
Last seen:
18 hours ago
Joined:
10 years, 10 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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Comment: C: Unable to install samtools in macOS Catalina
... nowadays this needs a version number otherwise it installs a wrong version and does not pull the proper libraries: conda install samtools==1.10 ...
written 15 days ago by Istvan Albert ♦♦ 84k
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Comment: C: Unable to install samtools in macOS Catalina
... rerun the installation, not so long ago conda developed a problem where it pulls the wrong version of samtools, the installation file has been recently updated to fix this error # Activate the bioinformatics enviroment. conda activate bioinfo # Install most bioinformatics tools c ...
written 15 days ago by Istvan Albert ♦♦ 84k
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Answer: A: 'make' is not recognized as an internal or external command, operable program or
... You would need to be running this in a Unix shell, all instructions refer to that environment. You can install the Linux Subsystem on Windows and run it through that. That being said, the code (in general) should run fine on Windows as well since Python is the only requirement. In that case, you ...
written 16 days ago by Istvan Albert ♦♦ 84k
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Comment: C: Conservative sequence search from same organism of different species?
... If you think about your question you'll realize that it is lacking specificity. In general for the same organism, the entire sequence is conserved, after all it is the identical organism. A variant between the two sequences of the same organism, however large, should not be indicative of "lack of c ...
written 17 days ago by Istvan Albert ♦♦ 84k
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Comment: C: Why does samtools mpileup skip positions?
... correct, add the -A flag and see if that fixes it, the next best quess is the BAQ cutoff. Alternatively, filter your BAM file for the location in question and look at the alignment properties over that location. ...
written 17 days ago by Istvan Albert ♦♦ 84k
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Comment: C: how to format the featurecounts output ?
... The manual states: > "When counting reads to meta-features (eg. genes) columns ‘Chr’, ‘Start’, ‘End’ and ‘Strand’ may each contain multiple values (separated by semi-colons), which correspond to individual features included in the same meta-feature." Note how it states that semi colon is used t ...
written 17 days ago by Istvan Albert ♦♦ 84k
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Answer: A: Why does samtools mpileup skip positions?
... the default invocation of the pileup command skips certain alignments that it deems unreliable. Alas, what gets skipped is not all that well documented. You need to figure out what filters are applied from the available flags: -A, --count-orphans do not discard anomalous read pairs -q ...
written 17 days ago by Istvan Albert ♦♦ 84k
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Answer: A: How to download seqret method in Linux?
... Use conda to install the `emboss` package. `seqret` is part of the `emboss` distribution: Install conda as described in: https://docs.conda.io/en/latest/miniconda.html then install `emboss` from the bioconda channel: conda install -c bioconda emboss test the package works: seqret -h p ...
written 17 days ago by Istvan Albert ♦♦ 84k
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Comment: C: how to format the featurecounts output ?
... the output for the lines with repeating sequence names seems incorrect. as I recall, the expected output of feature counts is simple and straightforward, the chromosome name is listed only once and it should not require the type of cleanup you seem to need is it possible that this file was crea ...
written 17 days ago by Istvan Albert ♦♦ 84k
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Comment: C: Find all NCBI taxids in some group (e.g., all coronaviruses)
... yes that is correct, but usually is not a good idea since getting the `xtract` usage right can be tedious. If the file is not saved one ends up having to rerun the query over and over again. Thus when using `xtract` I am trying to give the example in what I think is a more optimal workflow, where ...
written 18 days ago by Istvan Albert ♦♦ 84k

Latest awards to Istvan Albert

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Scholar 7 days ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: When To Choose Python Over Perl (And Vice Versa)?
Epic Question 10 days ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Scholar 12 days ago, created an answer that has been accepted. For A: Memory problem with RNA-SeQC jar (v1.1.8)
Scholar 12 days ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Scholar 25 days ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
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Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Scholar 11 weeks ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Sam File Format - Lesser Known Tips And Tricks
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: When To Choose Python Over Perl (And Vice Versa)?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: When To Choose Python Over Perl (And Vice Versa)?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Suggesting The Removal Of Post Closing
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: This Is A Test Poll
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
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

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