Admin: Istvan Albert

gravatar for Istvan Albert
Istvan Albert ♦♦ 74k
Reputation:
74,290
Status:
Trusted
Location:
University Park, USA
Website:
https://www.ialbert.me/
Scholar ID:
Google Scholar Page
Last seen:
1 day, 2 hours ago
Joined:
8 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 • 4,455 results • page 1 of 446 • next >
3
votes
1
answer
85
views
1
answers
Answer: A: Set maximum insert size with BWA MEM?
... I recommend that people don't rely on the "proper" flag. It is not a well-defined concept. Typically we never know for sure what is really going on. It is basically an illusion, where we give up control to the developer and assume that "proper" meant the same to them as for us. We never fully unde ...
written 2 days ago by Istvan Albert ♦♦ 74k
1
vote
1
answer
159
views
1
answers
Comment: C: A Theoretical Question About RNA-Seq Normalization
... You should specify the purpose of normalization. Why do you want to normalize these value in the first place? What comparisons do you intend to perform? In general, normalization should be performed to characterize samples where there is a reason to expect that the differences are few, isolated ...
written 2 days ago by Istvan Albert ♦♦ 74k
0
votes
2
answers
124
views
2
answers
Comment: C: metaphlan2.py [Errno 2] No such file or directory
... If it says it is not installed it means that it cannot see it the way it thinks it should be there. You should post this on the developer's website since it is them that the most knowledgeable and ought to assist you with it. In general, like I said these are the simplest problems to troubleshoot ...
written 2 days ago by Istvan Albert ♦♦ 74k
3
votes
2
answers
169
views
2
answers
Answer: C: HISAT2 index creation
... In your example, there are no splice junctions. Every exon is labeled as a distinct transcript id. Hence the script cannot produce splice junctions. I changed a few transcripts to have the same id, and now the script does produce splice sites on your data. ...
written 2 days ago by Istvan Albert ♦♦ 74k
1
vote
2
answers
153
views
2
answers
Answer: A: Longer scaffolds from multiple eukaryote genome assemblies
... I would imagine that you need to look outside the 'classic" field of high throughput sequencing. You most likely need a long read assembler that works off end-overlaps rather than the de Bruijn graph type of assemblers. For example this (I found this as a search so I can't comment on its applicabil ...
written 3 days ago by Istvan Albert ♦♦ 74k
3
votes
2
answers
124
views
2
answers
Answer: A: metaphlan2.py [Errno 2] No such file or directory
... This is the simplest but also often the most infuriating of all errors a program can raise. A file is missing. But which one ... alas, the program does not speak to that. Trace the error message through the source, if you have the same version as the source that seems to indicate that bowtie2 is ...
written 3 days ago by Istvan Albert ♦♦ 74k
0
votes
2
answers
169
views
2
answers
Comment: C: HISAT2 index creation
... The script here https://github.com/infphilo/hisat2/blob/master/hisat2_extract_splice_sites.py is a fairly simple line-oriented processing, you should be able to read through it and see what it does. It appears that it only requires the `exon` to be in the type then `transcript_id` and `gene_id` to ...
written 3 days ago by Istvan Albert ♦♦ 74k
1
vote
2
answers
239
views
2
answers
Comment: C: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
... The reason for scapegoating is that as long as p-values are permitted to be used, many/most don't feel the need to look for an alternative. ...
written 4 days ago by Istvan Albert ♦♦ 74k
0
votes
1
answer
122
views
1
answers
Comment: C: Change OTU names to taxon names
... I have tried to reformat your post to make it more readable. Please verify that the column formats that I ended up with conform to what you have. I would suggest to specify a simple but complete example. Where the result matches the input. In this case it does not seem to. Show the two inputs then ...
written 4 days ago by Istvan Albert ♦♦ 74k
2
votes
2
answers
169
views
2
answers
Answer: A: HISAT2 index creation
... While you seem to want to use the types interchangeably the unfortunate reality is that a GTF2 file is only remotely similar to a GFF3 file. The way the transcripts are encoded is different. Hence, unless the program was written to handle both you can't substitute one for the other. A GTF2 file w ...
written 4 days ago by Istvan Albert ♦♦ 74k

Latest awards to Istvan Albert

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Illumina'S New Reduced Resolution Q (Phred) Scores - Good Or Bad?
Scholar 2 days ago, created an answer that has been accepted. For A: Entrez.esearch url bug
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Is The Biostar Fading? (Updated For 2014)
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Illumina'S New Reduced Resolution Q (Phred) Scores - Good Or Bad?
Scholar 2 days ago, created an answer that has been accepted. For A: Entrez.esearch url bug
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Illumina'S New Reduced Resolution Q (Phred) Scores - Good Or Bad?
Commentator 4 days ago, created a comment with at least 3 up-votes. For C: Global Sequence Alignment
Scholar 11 days ago, created an answer that has been accepted. For A: Entrez.esearch url bug
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Am I Sabotaging Myself By Getting A Masters Instead Of A Phd?
Scholar 23 days ago, created an answer that has been accepted. For A: Entrez.esearch url bug
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Will Python Take The Place Of R?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Am I Sabotaging Myself By Getting A Masters Instead Of A Phd?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Entrez.esearch url bug
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Will Python Take The Place Of R?
Scholar 6 weeks ago, created an answer that has been accepted. For A: Entrez.esearch url bug
Librarian 6 weeks ago, created a post with more than 10 bookmarks. For Table Of Contents To All Review Paper Compilations On Biostar
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Appending Identifiers To The Fasta Header: Multiple Files
Great Question 9 weeks ago, created a question with more than 5,000 views. For Hadley Wickham of ggplot and RStudio uses this
Teacher 10 weeks 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 577 users visited in the last hour