Admin: Istvan Albert
Istvan Albert ♦♦ 80k
- Reputation:
- 80,400
- Status:
- Trusted
- Location:
- University Park, USA
- Website:
- https://www.ialbert.me/
- Scholar ID:
- Google Scholar Page
- Last seen:
- 22 hours ago
- Joined:
- 9 years, 9 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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... Code examples may be translated in any other language,
What is not permitted is re-publishing another version of the book where any of the content is copied verbatim and only the code is changed.
As always *Fair Use* applies and I consider myself a supporter of [Fair Use](https://en.wikipedia.or ...
written 15 days ago by
Istvan Albert ♦♦ 80k
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... I will say that de-duplication is a far more complex concept than what people/end users initially assume. Even interpreting the meaning of a deduplication plot is far from trivial - I had to give it two tries myself.
* https://www.biostars.org/p/83842/
* https://www.biostars.org/p/107402/
In the e ...
written 6 weeks ago by
Istvan Albert ♦♦ 80k
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Comment:
C: CIGAR inconsistency BWA/GATK
... your post is too long - too many unrelated details - makes too difficult to read and parse. What you should post instead is just the issue at hand (and don't post examples where there is no problem), for example post the CIGAR string the alignment itself like so:
2M2D2M
alignment:
AATTAA
...
written 6 weeks ago by
Istvan Albert ♦♦ 80k
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... As https://www.biostars.org/u/18713/ points out the right email is `contact@biostarhandbook.com`.
A short answer is that everything is included. ...
written 7 weeks ago by
Istvan Albert ♦♦ 80k
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... ok but look someone took the effort to answer your question. You should thank them and leave it be. It is still the correct answer to the question and we need to honor the effort that goes into answering questions. ...
written 9 weeks ago by
Istvan Albert ♦♦ 80k
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... deleting a post after getting a satisfactory answer is grounds for suspension! ...
written 9 weeks ago by
Istvan Albert ♦♦ 80k
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... See also Popoolation a tool
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232374/
...
written 9 weeks ago by
Istvan Albert ♦♦ 80k
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... Ok, now I understand better what you are doing (after reading further down the line).
This is really not about error correcting (as the title puts it) but it is about how to analyze very a short sequence that has been measured millions of times with the goal to identify rare mutations - where the ...
written 9 weeks ago by
Istvan Albert ♦♦ 80k
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... You are posting about a tool that does "statistical plotting". The documentation has a screenshot of the data, a screenshot of the UI but does not show what the generated plot looks like ... shouldn't that be the first thing you show?
Then it looks like your code is basically a wrapper around the P ...
written 9 weeks ago by
Istvan Albert ♦♦ 80k
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... The way I see it you are over-engineering a problem that has already been solved - and with that, you are making the process less precise and accurate.
{edited} - not relevant advice as I did not fully understand the OPs problem layout. SNP callers are not quite ready to call variation on data of t ...
written 9 weeks ago by
Istvan Albert ♦♦ 80k
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