Admin: Istvan Albert

gravatar for Istvan Albert
Istvan Albert ♦♦ 85k
Reputation:
85,350
Status:
Trusted
Location:
University Park, USA
Website:
https://www.ialbert.me/
Scholar ID:
Google Scholar Page
Last seen:
16 hours ago
Joined:
11 years, 1 month 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

<prev • 4,937 results • page 2 of 494 • next >
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Answer: C: Downloading SRA data
... If you intend to work in bioinformatics install the Linux Subsystem and work from there. There is no point in puttering around in windows prompt, sooner rather than later you'll have to use Unix anyway ...
written 4 days ago by Istvan Albert ♦♦ 85k
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Comment: C: How to download multiple SRA files with prefetch in ubuntu?
... prefetch does not unpack the files, just prefetches them (places them in a storage system for later commands that need it) if you want to see files you need to use `fastq-dump` ...
written 6 days ago by Istvan Albert ♦♦ 85k
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Comment: C: Align pacbio subreads against assembled pacbio reads
... whoops https://www.biostars.org/u/23882/ beat me to it ...
written 6 days ago by Istvan Albert ♦♦ 85k
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Answer: A: Align pacbio subreads against assembled pacbio reads
... I would recommend minimap2, it has modes for pacbio as well. ...
written 6 days ago by Istvan Albert ♦♦ 85k
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Comment: C: Problem with bedtools intersect with two gtfs
... perhaps because the order of the attributes is unexpected? in the file you have `gene_id` followed by `transcript_id`, the warning shows it flipped. It shouldn't matter but it might. (BTW including the a few lines from the data instead of images would make more sense) ...
written 9 days ago by Istvan Albert ♦♦ 85k
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Answer: A: Name of the consensus fasta sequence from a Minimap + Samtools alignment
... Renaming fasta ids is probably straightforward to automate: cat foo.fa >foo AAAAA then: cat foo.fa | seqret --filter -sid bar >bar AAAAA or: cat foo.fa | seqkit replace -p foo -r bar >bar AAAAA and probably many other solutions exist ...
written 12 days ago by Istvan Albert ♦♦ 85k
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Comment: C: Why it is not use UMIs for RNA-seq?
... I always imagined (never thought it through in detail so far) that the limitation was that you would need to PCR amplify DNA to attach UMIs. In single-cell RNAseq there is sufficient material before amplification, but for single-cell DNA there wouldn't be. Thus one would not benefit that greatly fro ...
written 15 days ago by Istvan Albert ♦♦ 85k
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Answer: A: Biopython: Module not found after new install of Python 3.8.1
... usually the reason for such errors is that pip runs a different version of python than the one that you start when you invoke python directly at the command line. Try to run pip like this: python -m pip to ensure the same python is executed when running pip ...
written 16 days ago by Istvan Albert ♦♦ 85k
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Answer: A: Help me in PANTHER
... It says there that you need to log in to select from that list. Try that see if it works. ...
written 18 days ago by Istvan Albert ♦♦ 85k
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Comment: C: Two bams with similar flagstat output have very different file size
... thanks for following up, the best questions/answers are those that everyone learns something from ...
written 21 days ago by Istvan Albert ♦♦ 85k

Latest awards to Istvan Albert

Scholar 6 days ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Good Answer 13 days ago, created an answer that was upvoted at least 5 times. For A: bwa mem and multiply mapped reads
Scholar 28 days ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Teacher 5 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?
Epic Question 7 weeks ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this
Great Question 11 weeks ago, created a question with more than 5,000 views. For Heng Li of BWA and Samtools uses this
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Scholar 11 weeks ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Scholar 3 months ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: When To Choose Python Over Perl (And Vice Versa)?
Epic Question 3 months ago, created a question with more than 10,000 views. For Hadley Wickham of ggplot and RStudio uses this
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: This Is A Test Poll
Scholar 3 months ago, created an answer that has been accepted. For A: Memory problem with RNA-SeQC jar (v1.1.8)
Scholar 3 months ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?
Scholar 4 months ago, created an answer that has been accepted. For A: Set Default Sort Order of Posts?

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