Admin: 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 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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... 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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... 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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... 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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... 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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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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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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... 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
1
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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
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