Admin: Istvan Albert
Istvan Albert ♦♦ 77k
- Reputation:
- 76,590
- Status:
- Trusted
- Location:
- University Park, USA
- Website:
- https://www.ialbert.me/
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 2 hours ago
- Joined:
- 8 years, 8 months ago
- Email:
- i************@gmail.com
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: Does BWA mem ever edit data
... It is not the right question - BWA produces a SAM format - so the question should be "Is the sequence information in a SAM format identical to the FASTQ sequence" - to which the answer is NO. The SAM format represents information on the forward strand, hence sequences mapping on the reverse strand w ...
written 8 days ago by
Istvan Albert ♦♦ 77k
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... Single cell sequencing is a topic I would like to add - but the field feels quite un-settled: for example, *which RNA-Seq should we use?* ... fifty publications later, *well well well maybe we should use the same as regular RNA-Seq*... really? hard to believe...
All content in the book comes from p ...
written 15 days ago by
Istvan Albert ♦♦ 77k
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... Thanks for the kind words. I am happy to hear that the resources are effective.
You are right that we ought to have a forum of some sorts - especially since now the site hosts a book and two courses all going in parallel. We are working on addressing this shortcoming. We will likely have a forum in ...
written 6 weeks ago by
Istvan Albert ♦♦ 77k
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... I believe that as long as the accession numbers are the same you'd get the same behavior, hence you would not need to do anything in particular. My expectation is that the blast TaxDB is indexed by accession numbers.
If you also wanted to build your own custom taxonomy - then you'd have to build i ...
written 9 weeks ago by
Istvan Albert ♦♦ 77k
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... The content is the same at any given time point for both editions. Moreover, readers may keep the last PDF and eBook version they have access to. Thus student edition owners would get access to the version released six months from now as well. What they would not be able the access is the website an ...
written 9 weeks ago by
Istvan Albert ♦♦ 77k
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... Since with Kallisto you are quantifying against transcripts hence you can go ahead with your analysis.
If you trying to discover new splice variants you would need to align against the genome with a different method. ...
written 9 weeks ago by
Istvan Albert ♦♦ 77k
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... A mapping quality of zero usually indicates a multiply mapped read (one that aligns equally well in multiple locations). The alignments often indicate the other locations, but in this case, they do not. The flag 272 has more information
0x110 272 REVERSE,SECONDARY
See how this alignment is a s ...
written 10 weeks ago by
Istvan Albert ♦♦ 77k
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... You have to have to download the taxonomy database as well. You can use the update script for that:
update_blastdb.pl taxdb --decompress
Then ensure that blast can automatically access that information as well:
export BLASTDB=$BLASTDB:~/location/of/taxdb
...
written 10 weeks ago by
Istvan Albert ♦♦ 77k
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... Your descriptions in general and the presentation of the service itself suffers greatly from wrong kind of specificity. THere is little information about your service from the point of view of what an end user needs.
This has nothing to do with it being a "early" attempt or not.
There is a lack o ...
written 10 weeks ago by
Istvan Albert ♦♦ 77k
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... In what sense is FTP:
> great protocol to simultaneously connect to multiple databases at once and search them in parallel
what do you mean by "searching via FTP"? AFAIK FTP has no support for searching. ...
written 10 weeks ago by
Istvan Albert ♦♦ 77k
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For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers
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For C: A Farewell To Bioinformatics
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For A: bwa mem and multiply mapped reads
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For A: bwa mem and multiply mapped reads
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