Admin: Istvan Albert

gravatar for Istvan Albert
Istvan Albert ♦♦ 84k
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Location:
University Park, USA
Website:
https://www.ialbert.me/
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Google Scholar Page
Last seen:
3 hours ago
Joined:
10 years, 9 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: bowtie2 '-a' does not return all alignments
... Short read aligners were never designed to be mathematically optimal or to produce all equally scoring alignments. Thus I would not recommend using that for this type of use cases. ...
written 1 day ago by Istvan Albert ♦♦ 84k
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Answer: A: summury control quality assembly the all genome sequencing
... MultiQC can parse the output of several different tools and collate them into one report https://multiqc.info/ ...
written 2 days ago by Istvan Albert ♦♦ 84k
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Comment: C: -m option of HTSeq in featureCounts
... you should think about why you want that to be set and what it actually means in the larger context. why would you want that parameter to be set? is it because you want one feature to be fully covered, or completely included? etc perhaps other parameters of `featureCounts` do an even better job ac ...
written 3 days ago by Istvan Albert ♦♦ 84k
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Comment: C: Does BWA MEM understand paired-end suffixes? /2 in a single FASTQ file?
... Ah indeed, that was it. All I remember that it drove me nuts when the reads got out of sync and for a time I couldn't quite figure out why. ...
written 4 days ago by Istvan Albert ♦♦ 84k
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Answer: A: -m option of HTSeq in featureCounts
... featureCounts does not implement all the features of htseq-counts. Conceptually the tool works differently and uses different internal representations. I don't think that the `intersection-nonempty` mode is implemented. ...
written 4 days ago by Istvan Albert ♦♦ 84k
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Answer: A: Comparing SPAdes assemblies to each other?
... See if using the interactive dot plotter works for your case. I recently discovered this implementation of dot plotting and found extremely usefuyl. It uses nucmer alignments hence it is quite performant (unlike most dot plotters), plus it is interactive and fast https://dnanexus.github.io/dot/ ...
written 4 days ago by Istvan Albert ♦♦ 84k
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Answer: A: BBMap Statistics Evaluation
... I don't know what BBMap does specifically, but typically the denominator is the total number of reads, or the total number of mapped reads, depending on the circumstance. In this case, it seems that the total number of reads was not reported in the statistics, hence we can't check that assumption. ...
written 4 days ago by Istvan Albert ♦♦ 84k
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Answer: A: Does BWA MEM understand paired-end suffixes? /2 in a single FASTQ file?
... As far as I know samtools does not have `bam2fq` subcommand . It does have a `fastq` subcommand that will generate fastq files. When it comes to mapping use two different files rather than an interleaved one. I will also mention that the way the `fastq` command works for when producing a singl ...
written 4 days ago by Istvan Albert ♦♦ 84k
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Comment: C: Transcriptome analysis of two closely related plant species
... If TIN numbers don't look good you should perform a gene level analysis. If the transcripts are not covered evenly the data won't be able to reliably distinguish between different transcripts. ...
written 4 days ago by Istvan Albert ♦♦ 84k
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Answer: C: Transcriptome analysis of two closely related plant species
... I would look into the concept called transcript integrity (TIN) to evaluate how well do the reads conform to the transcripts across both species, if the TIN numbers look good and most transcripts are covered you could get meaningful results without assembling anything. You can compute TIN with the ...
written 4 days ago by Istvan Albert ♦♦ 84k

Latest awards to Istvan Albert

Teacher 15 days ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Scholar 6 weeks ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Sam File Format - Lesser Known Tips And Tricks
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: When To Choose Python Over Perl (And Vice Versa)?
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Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Suggesting The Removal Of Post Closing
Great Question 8 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
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Scholar 10 weeks ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
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Great Question 11 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Scholar 11 weeks ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
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