Admin: Istvan Albert
Istvan Albert ♦♦ 84k
- Reputation:
- 84,030
- Status:
- Trusted
- Location:
- University Park, USA
- Website:
- https://www.ialbert.me/
- Scholar ID:
- Google Scholar Page
- Last seen:
- an hour ago
- Joined:
- 10 years, 10 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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... If what you are asking is whether you can compare control and treatment across different experiments then the answer is that you have to more careful (while you are doing it) and more transparent (when disseminating the results) about what you are doing.
The statistical power of most methods will b ...
written 3 hours ago by
Istvan Albert ♦♦ 84k
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... See this issue as well:
https://github.com/biostars/biostar-handbook-issues/issues/123 ...
written 3 days ago by
Istvan Albert ♦♦ 84k
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... 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 3 days ago by
Istvan Albert ♦♦ 84k
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... 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 3 days ago by
Istvan Albert ♦♦ 84k
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... 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 4 days ago by
Istvan Albert ♦♦ 84k
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... 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 5 days ago by
Istvan Albert ♦♦ 84k
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... 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 5 days ago by
Istvan Albert ♦♦ 84k
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... 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 5 days ago by
Istvan Albert ♦♦ 84k
1
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... 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 5 days ago by
Istvan Albert ♦♦ 84k
1
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... 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 5 days ago by
Istvan Albert ♦♦ 84k
Latest awards to Istvan Albert
Scholar
12 days ago,
created an answer that has been accepted.
For A: Set Default Sort Order of Posts?
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For bam.iobio realtime sampling to generate global statistics of your bam file in a few seconds
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: Set Default Sort Order of Posts?
Good Answer
9 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Sam File Format - Lesser Known Tips And Tricks
Good Answer
9 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
11 weeks ago,
created an answer that was upvoted at least 5 times.
For A: When To Choose Python Over Perl (And Vice Versa)?
Commentator
12 weeks ago,
created a comment with at least 3 up-votes.
For C: Suggesting The Removal Of Post Closing
Great Question
12 weeks 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?
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?
Scholar
3 months ago,
created an answer that has been accepted.
For A: Set Default Sort Order of Posts?
Great Question
3 months ago,
created a question with more than 5,000 views.
For Heng Li of BWA and Samtools uses this
Popular Question
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created a question with more than 1,000 views.
For Pablo Cingolani of snpEff uses this
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4 months ago,
created an answer that has been accepted.
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For Fastq Quality Control Shootout
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