Admin: Istvan Albert

gravatar for Istvan Albert
Istvan Albert ♦♦ 82k
Reputation:
81,820
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Trusted
Location:
University Park, USA
Website:
https://www.ialbert.me/
Scholar ID:
Google Scholar Page
Last seen:
19 hours ago
Joined:
10 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 • 4,698 results • page 1 of 470 • next >
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Answer: A: how to fix INVALID_FLAG_MATE_UNMAPPED sam flag
... I think the right solution is probably to read your files with a programming interface like Pysam and work out the issues that way. https://pysam.readthedocs.io/en/latest/api.html ...
written 14 days ago by Istvan Albert ♦♦ 82k
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Comment: C: how to fix INVALID_FLAG_MATE_UNMAPPED sam flag
... Is it possible that you have two reads with the same name (since it is paired) and the other raises the error? Also see if `bam2bed` followed by a `bed2bam` would work (`bedtools`) ...
written 14 days ago by Istvan Albert ♦♦ 82k
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Comment: C: What % of rRNA contamination is acceptable?
... The problem here goes much deeper. Simply put most statistical methods cannot account for the type of errors you observe. The concept of transcript integrity as described here: http://rseqc.sourceforge.net/#tin-py is the closest to what you might be after. What you want is to filter not just for ...
written 14 days ago by Istvan Albert ♦♦ 82k
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Answer: A: Why the proportion of reads with adapters in NGS is low?
... The "normal" expectation for NGS data is that no reads have adapters in them. The explanation for not having adapters is that the DNA fragment is longer than the read length. The "typical" adapter read-through is an "error" that happens when the instrument gets a DNA fragment that is too short. U ...
written 15 days ago by Istvan Albert ♦♦ 82k
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Comment: C: What % of rRNA contamination is acceptable?
... I would say that the data shows too many reads in the intronic regions (your second image) - 10 to 20% of the exonic read counts are present. Also, there is unexpectedly weird fragmentation throughout - coverages drop the zero in the middle of the exon. ...
written 15 days ago by Istvan Albert ♦♦ 82k
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Comment: C: Command prompts combination
... It is not clear what you are saying here, the commands do work separately but not when giving the command together? In what way does it not work? Do one step at a time, see if you can get it to work - most importantly the files need to be sorted by the field that you join on. ...
written 16 days ago by Istvan Albert ♦♦ 82k
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Answer: A: Is it possible to use LC_ALL=C on a blast command?
... Don't put `LC_ALL=C` as a parameter to blast! That won't work. You can set LC_ALL=C before a command: LC_ALL=FOO; echo $LC_ALL prints: FOO it gets applied to all commands run in that shell. The best recommendation would be to export the variable in bash (preferable upon initialization ...
written 17 days ago by Istvan Albert ♦♦ 82k
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Comment: C: What % of rRNA contamination is acceptable?
... take a screenshot of a gene/transcript that comes up differentially expressed and show it here. show the coverages for both tracks the control and condition, here is an example (host with imgur): ![enter image description here][1] [1]: https://i.imgur.com/BRuwP7a.png ...
written 17 days ago by Istvan Albert ♦♦ 82k
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Comment: C: Paired end for minia
... This sounds like there may be contaminations and other errors in the data. As you add more data the number of systematic errors increases. It also often happens that the second in pair is worse in quality (though nowadays that is rarer). Evaluate your data with FastQC, see if you need to clean it u ...
written 18 days ago by Istvan Albert ♦♦ 82k
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Comment: A: Paired end for minia
... Don't concatenate the reads. If you believe that the reads overlap use a tool that merges your paired-end reads into one. ...
written 18 days ago by Istvan Albert ♦♦ 82k

Latest awards to Istvan Albert

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Popular Question 12 days ago, created a question with more than 1,000 views. For Pablo Cingolani of snpEff uses this
Epic Question 12 days ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this
Scholar 15 days ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Great Question 6 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Epic Question 6 weeks ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How Do I Map, Align, And Plot My Solid Results?
Great Question 8 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Do You Like Ipython Notebook?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Do You Like Ipython Notebook?
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: A Farewell To Bioinformatics
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: A Farewell To Bioinformatics
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Fastqc for RNA-Seq data (Illumina 1.9)
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: A Farewell To Bioinformatics
Scholar 11 weeks ago, created an answer that has been accepted. For A: Is it allowed to make a derivative work of the BioStar Handbook in another progr
Gold Standard 3 months ago, created a post with more than 25 bookmarks. For Table Of Contents To All Review Paper Compilations On Biostar
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How to align Trimmomatic unpaired reads with BWA?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Do You Like Ipython Notebook?
Scholar 3 months ago, created an answer that has been accepted. For A: Is it allowed to make a derivative work of the BioStar Handbook in another progr
Scholar 3 months ago, created an answer that has been accepted. For A: How to align Trimmomatic unpaired reads with BWA?
Scholar 3 months ago, created an answer that has been accepted. For A: Is it allowed to make a derivative work of the BioStar Handbook in another progr
Scholar 3 months ago, created an answer that has been accepted. For A: Is it allowed to make a derivative work of the BioStar Handbook in another progr
Great Question 4 months ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this

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