Admin: Istvan Albert
Istvan Albert ♦♦ 77k
- Reputation:
- 77,310
- Status:
- Trusted
- Location:
- University Park, USA
- Website:
- https://www.ialbert.me/
- Scholar ID:
- Google Scholar Page
- Last seen:
- an hour ago
- Joined:
- 9 years 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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The best way to understand your data is to separate your BAM file into two, one that contains only reads from file 1 the other only reads from file 2 (basically you are breaking the pairs).
samtools view -fb 64 all.bam > read1.bam
samtools view -Fb 64 all.bam > read2.bam
Now all ...
written 1 hour ago by
Istvan Albert ♦♦ 77k
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... Use fastq-dump to get your SRA data, I don't trust mirrors that much actually...
fastq-dump --split-files -X 1000 SRR5959411
gives me one file, this gives two files
fastq-dump --split-files -X 1000 SRR5969329
the sizes are right, as expected paired and 76bp
seqkit stat *.fastq
lik ...
written 3 hours ago by
Istvan Albert ♦♦ 77k
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... The problem is best formulated in terms of programming paradigms as a choice between
- *imperative* (procedural) programming that uses constructs such as `if`, `for`, `while` versus
- *functional* (declarative) programming that has functions such as `map`, `filter`, `reduce` (using Python as la ...
written 7 days ago by
Istvan Albert ♦♦ 77k
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... My point is that there is a responsibility that toolmakers have to properly document and make a note of situations that might lead to misunderstandings. It is insufficient to point to the documentation (fine print).
Especially in the light that this was noted in 2015, most people that can be consi ...
written 9 days ago by
Istvan Albert ♦♦ 77k
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... Considering how widely BLAST is used and how often people filter on e-values no wonder that we have an irreproducibility problem in life sciences
...
written 9 days ago by
Istvan Albert ♦♦ 77k
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... Recommendation: show the alignments as text and not images
also remove the unnecessary data listings, those make the post difficult to follow
...
written 9 days ago by
Istvan Albert ♦♦ 77k
0
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... now that I looked at it in more detail there is more to it, the "bug" or "behavior" is triggered only in some special cases.
> In some cases a final HSP will improve enough in the later gapped phase to rise to the top hits.
You have to have an alignment that matches the statement above.
Look ...
written 12 days ago by
Istvan Albert ♦♦ 77k
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... now that I read the report a little better - I want to mention that my example here may not trigger the bug. As the response from [NCBI reply states](https://gist.github.com/sujaikumar/504b3b7024eaf3a04ef5)
> In some cases a final HSP will improve enough in the later gapped phase to rise to the ...
written 12 days ago by
Istvan Albert ♦♦ 77k
0
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... IMO that recommendation is still kind of suspicious - it either works as we think it does or not - this sort of special cases are even worse (if it worked one way in some cases and the other way in some others)
that being said I cannot reproduce the behavior either:
# Get the 16S Microbial dat ...
written 12 days ago by
Istvan Albert ♦♦ 77k
1
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1
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407
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... the paper states that the order is set by the order in the database, hence if you have the "right" order relative to the search the parameter will have no effect.
To verify what the paper states take the best hit that you have, move it last in the FASTA file, reindex with blast and test again
...
written 14 days ago by
Istvan Albert ♦♦ 77k
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For A: Where To Look For Quality Bioinformatics Short Courses And Workshops?
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For bam.iobio realtime sampling to generate global statistics of your bam file in a few seconds
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For A: How Do I Convert From Bed Format To Gff Format?
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For A: How To Grep Largest Contig From A Multi Fasta File
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For A: Extracting Reads That Are Properly Paired From Bam File
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For C: A Farewell To Bioinformatics
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