Admin: Istvan Albert

gravatar for Istvan Albert
Istvan Albert ♦♦ 73k
Reputation:
73,250
Status:
Trusted
Location:
University Park, USA
Website:
https://www.ialbert.me/
Scholar ID:
Google Scholar Page
Last seen:
3 hours ago
Joined:
7 years, 11 months 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

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Comment: C: RNA-seq RPKM >=1 increases after downsampling but RPKM >= 0.1 decreases after do
... Any chi-square tool will do, there are many online, that you could use. What you are testing for is whether the pairs 12979 20311 13247 18847 could be consistent with a random sampling. ...
written 5 days ago by Istvan Albert ♦♦ 73k
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Answer: A: Predict the effect of SNPs in a VCF file generated using a Trinity assembly
... You can build custom annotations for SnpEff from a GFF file: http://snpeff.sourceforge.net/SnpEff_manual.html#databases ...
written 6 days ago by Istvan Albert ♦♦ 73k
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Comment: C: Biostar under spam attack - restrictions added to post content and title
... I'll be our for a few hours but I'll see what we can do later this evening. Thanks for the hard work, these spammers seem to be defeating the captchas' which means they have to put in some effort and hopefully getting banned will make it clear that is not worth it. ...
written 6 days ago by Istvan Albert ♦♦ 73k
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Answer: A: RNA-seq RPKM >=1 increases after downsampling but RPKM >= 0.1 decreases after do
... The random sampling means that your numbers will vary, they have to as there is a chance of hitting transcripts unevenly. Even without running a chi-square test I'd say that your numbers fall well into the expected range of variation. ...
written 6 days ago by Istvan Albert ♦♦ 73k
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Comment: C: Retrieve all ids from NCBI
... Amusingly after doing some investigation, I came to believe that a wildcard search at NCBI does not do what you and I and most people think that a wildcard search should be doing. What it does instead is that it creates an expanded search query that includes all terms that match the wildcard. So `P ...
written 7 days ago by Istvan Albert ♦♦ 73k
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Comment: C: Retrieve all ids from NCBI
... Interesting, the perils of matching on names. Good to know. ...
written 7 days ago by Istvan Albert ♦♦ 73k
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Comment: C: Retrieve all ids from NCBI
... I wondered just how many bioprojects are there in total. Running the search on its own tells us that: esearch -query "P*" -db bioproject prints: bioproject NCID_1_18646926_130.14.22.215_9001_1505146040_1821616193_0MetA0_S_MegaStore_F_1 1 10454 1 so the ...
written 7 days ago by Istvan Albert ♦♦ 73k
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Comment: C: True score of alignment BWA-MEM
... I vaguely recall reading a statement either in the (BWA manual or the SAM spec) though I am unable to find it now, how the alignment score may not match the MD tag or CIGAR strings. It struck me as odd, back then but has to do with the way things work. CIGAR and MD can be determined faster than an a ...
written 11 days ago by Istvan Albert ♦♦ 73k
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Answer: A: True score of alignment BWA-MEM
... The alignment that I get with `bwa` do contain the `AS` tags. So it is strange that yours do not. samtools view -H http://data.biostarhandbook.com/bam/demo.bam | grep PG prints: @PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem /Users/ialbert/refs/ebola/2014.fa SRR1553425_1.fastq SRR1553 ...
written 11 days ago by Istvan Albert ♦♦ 73k
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Answer: A: Demultiplexing fastq.gz files
... You can't use bcl2fastq for this. The bad news is that there might not be a tool to do as it is a task that is usually handled at the instrument level so there is less of a need to do it. You would probably need to use a tool designed for cutting adapters to filter the reads: http://cutadapt.read ...
written 11 days ago by Istvan Albert ♦♦ 73k

Latest awards to Istvan Albert

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: My Friend Anthony Made This Cool Mini-Site To Find A Freelance Bioinformatics Jo
Great Question 10 days ago, created a question with more than 5,000 views. For Hadley Wickham of ggplot and RStudio uses this
Scholar 11 days ago, created an answer that has been accepted. For A: Entrez.esearch url bug
Good Answer 13 days ago, created an answer that was upvoted at least 5 times. For A: What is the reason for most software errors in Bioinformatics according to you?
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Data Management System For Bioinformatics?
Scholar 24 days ago, created an answer that has been accepted. For A: Entrez.esearch url bug
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: What is the reason for most software errors in Bioinformatics according to you?
Epic Question 4 weeks ago, created a question with more than 10,000 views. For Rna-Seq Review Papers
Scholar 8 weeks ago, created an answer that has been accepted. For A: Entrez.esearch url bug
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to check if specific mutations are or not enriched in a RNAseq data seq?
Scholar 8 weeks ago, created an answer that has been accepted. For A: Entrez.esearch url bug
Prophet 9 weeks ago, created a post with more than 20 followers. For Table Of Contents To All Review Paper Compilations On Biostar
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Experienced Bioinformatics Analyst, Bioinformatics Consulting Center, Pennsylvan
Scholar 9 weeks ago, created an answer that has been accepted. For A: How to check if specific mutations are or not enriched in a RNAseq data seq?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Comments Left Inappropriately As Answers To A Question

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