Admin: Istvan Albert

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Istvan Albert ♦♦ 71k
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70,760
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Location:
University Park, USA
Website:
https://www.ialbert.me/
Scholar ID:
Google Scholar Page
Last seen:
20 hours ago
Joined:
7 years, 8 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

<prev • 4,248 results • page 1 of 425 • next >
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Comment: C: Inconsistency Between Cufflinks And Cuffdiff
... The choice needs to be made based on the phenomena under study - for example, once you establish that there is indeed a novel transcript variant then it makes sense to use that. Though clearly when doing so there will be a higher burden of proof as one now needs to both establish that the new tran ...
written 1 day ago by Istvan Albert ♦♦ 71k
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Comment: C: Read fragments receive maximum MAPQ in bowtie2
... the alignment that you list above is not a fragment, it is a full read match note `19M` nothing was clipped off. You have a mismatch in that `19M` but that's about it. ...
written 1 day ago by Istvan Albert ♦♦ 71k
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Answer: A: From bam paired files to fasta
... Manually merging contigs from mapped reads is a complicated task that is conceptually closest to what is called "consensus calling". Better alternatives might be to 1. perform a denovo assembly of the reads that will give you long contigs that can be annotated alter 2. call SNPs (variation) from t ...
written 2 days ago by Istvan Albert ♦♦ 71k
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Comment: C: Inconsistency Between Cufflinks And Cuffdiff
... We have to keep the coordinates for genes separate from the coordinates of transcripts. The only statement that we can infer is that the transcript comes from within the gene coordinates. But the gene coordinates tell us very little about the transcript coordinates. If most reads map to a region th ...
written 2 days ago by Istvan Albert ♦♦ 71k
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Answer: A: Pipeline suggestions for GO & pathway analysis for species without reference gen
... There is also "Annotate Dammit" - amusing (but somewhat questionable) tool name https://github.com/camillescott/dammit ...
written 2 days ago by Istvan Albert ♦♦ 71k
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Answer: A: Inconsistency Between Cufflinks And Cuffdiff
... The two operate a little differently when you use cufflinks you also assemble new transcripts and the quantification will include those as well. In this case, your data might contains read that while fall within a gene start/end do not match known annotation information - hence when using cuffdiff ...
written 2 days ago by Istvan Albert ♦♦ 71k
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Answer: A: Gene length fro GFF file to count RPKM for edgeR-RNA-seq analysis
... A gene level analysis typically considers transcripts formed by the concatenation of all exons of a gene (even if such transcript did not exist in reality). For the RPKM calculation the length of this transcript is required. This can be computed as the sum of the lengths of all exons. The start an ...
written 2 days ago by Istvan Albert ♦♦ 71k
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Comment: C: Multiple sam to bam followed by raw read count
... replace the text within the single quotes with the command you wish to execute. In general, when someone helps you with an advice you need to make a concerted effort to understand what the content consists of and how it works - that way it is easy to generalize and apply to a different situation. ...
written 2 days ago by Istvan Albert ♦♦ 71k
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Comment: C: Multiple sam to bam
... I would not recommend this post as it references an old version of samtools and the commands listed might not work anymore. ...
written 3 days ago by Istvan Albert ♦♦ 71k
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Answer: A: Multiple sam to bam
... You can add all your flags into a single command. In addition, the latest samtools does not even need the `-S` flag as it detects the input type automatically. samtools view -F 4 -b data.sam > data.bam To run all of these commands on all SAM file you could automate with: ls *.sam | xa ...
written 3 days ago by Istvan Albert ♦♦ 71k

Latest awards to Istvan Albert

Teacher 2 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
Scholar 3 days ago, created an answer that has been accepted. For A: bam to fasta
Teacher 3 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
Commentator 3 days ago, created a comment with at least 3 up-votes. For C: What Are The Open Source Alternatives To Gatk?
Commentator 11 days ago, created a comment with at least 3 up-votes. For C: What Are The Open Source Alternatives To Gatk?
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